Mutant MT-SP1 proteases with altered substrate specificity or activity

ABSTRACT

MT-SP1 mutein proteases with altered specificity for the target molecules they cleave can be used to treat human diseases, such as cancer. Cleaving VEGF or VEGFR at certain substrate sequences with wild-type and mutein MT-SP1 proteases can be used to treat pathologies associated with angiogenesis.

RELATED APPLICATIONS

Benefit of priority is claimed to U.S. provisional application Ser. No.60/561,720, filed Apr. 12, 2004, entitled “CLEAVAGE OF VEGF RECEPTOR BYWILDTYPE AND MUTANT MTSP1” to Ruggles et al. The subject matter of thisapplication is incorporated by reference in it entirety.

BACKGROUND OF THE INVENTION

The process of angiogenesis is central to the pathology of conditionsincluding malignancy, diabetic retinopathy and macular degeneration.That cancer is angiogenesis-dependent has been recently supported byexperimentation in which striking inhibition of tumor growth can beachieved not by direct treatment of the tumor, but rather by selectiveinhibition of the endothelial growth factor Vascular Endothelial GrowthFactor (VEGF). VEGF is an endothelial cell-specific mitogen normallyproduced during embryogenesis and adult life. VEGF functions as asignificant mediator of angiogenesis in a variety of normal andpathological processes, including tumor development. Tumorvascularization is a vital process for the progression of a tumor to astage from which it can metastasize. Three high affinity cognate VEGFreceptors (VEGFRs) have been identified: VEGFR-1/Flt-1,VEGFR-2/Flk-1/KDR, and VEGFR-3/Flt-4.

VEGFRs are cell surface receptor tyrosine kinases that function assignaling molecules during vascular development. An observation commonin pre-clinical studies of anti-angiogenic agents targeting VEGF hasbeen potent and broad-spectrum inhibition of very diverse tumor types(solid tissue and hematological), which is consistent with thewidespread dependence of cancer on angiogenesis irrespective of tissueof origin. Single i.v. injections of adenoviruses expressing solubleFlk1 and Flt1 transduce the liver, express high plasma levels, andsequester VEGF from its native receptors on endothelial cells. Thesecirculating VEGF receptors produce systemic inhibition of angiogenesisin corneal micropocket assays, and importantly produce strong andbroad-spectrum inhibition of tumor angiogenesis and tumor growth inestablished lung, prostate, colon, brain and pancreas tumors insubcutaneous, orthotopic and transgenic models. See, e.g. Kuo et al.2001 PNAS 98: 4605-10. Recently, the efficacy of anti-angiogenic therapyhas been demonstrated in a randomized phase III trial using theanti-VEGF monoclonal AVASTIN™ (Genentech) to treat patients withmetastatic colon cancer, thus providing proof of principle for thistreatment strategy in human neoplasia.

SUMMARY OF THE INVENTION

Nature has engineered the hundreds of proteases in the human genome toexquisite definition so that specificity, inhibition and hydrolysis areperfectly matched to physiological niche. While it has been shown thatsome proteases are down regulated in cancer, to date no naturalproteases are known to function in defending the body fromtumorigenesis. However, there are clear applications of proteasesprogrammed to hydrolyze proteins necessary for cancer growth. Thisinvention pairs structure-based protein engineering techniques withpositional scanning synthetic combinatorial library (PSSCL) assays toprovide novel serine proteases with specificity that, collectively,match the VEGF-R2 stalk over an extended region. PSSCL profiling is aproprietary technology that generates a complete substrate specificityprofile or “fingerprint” of each engineered protease in a single assay.With this technology, it is now possible to identify therapeuticallyrelevant proteases that have enhanced specificity toward targetsubstrates and little to no activity towards wild type substrates. Inthe design process, hundreds of proteases with altered specificityprofiles are produced. The technology offers an unprecedentedopportunity to study the structural features of specificity. With ascreening of proteases with PSSCL, the determinants of serine proteaseselectivity and catalytic efficiency can be identified. They offer notonly an opportunity to discover fundamental rules concerning serineprotease function, but also additional information for the design oftherapeutically relevant molecules.

The present invention provides compositions and methods for usingproteases that cleave proteins known to be involved in disease. Inparticular, wild type and mutein membrane type serine protease-1(MT-SP1) polypeptides are provided that cleave VEGF or VEGF receptor,which is known to be involved in angiogenesis. The resultant modifiedproteins are provided for use as agents for in vivo therapy of cancersand other angiogenesis-related pathologies, including but not limited tomacular degeneration, inflammation and diabetes.

The invention also provides methods for the modification of proteases toalter their substrate sequence specificity, so that the modifiedprotease specifically cleaves a VEGF or VEGF receptor protein. Cleavageof targeted VEGF or VEGFRs is provided for treatment of a broad range ofcancers wherein the treatment results in reduction or inhibition ofvascularization necessary for continued tumor growth. In one embodimentof the invention, this modified protease is a serine protease. Inanother embodiment of the invention, this modified protease is a muteinMT-SP1.

One embodiment of the invention involves generating a library ofprotease sequences to be used to screen for modified proteases thatcleave VEGF or a VEGFR at a desired substrate sequence. In one aspect ofthis embodiment, each member of the library is a protease scaffold withat least one mutation made to each different member of the proteaselibrary. The remainder of the protease scaffold has the same or asimilar sequence to wild-type MT-SP1 protease. The cleavage activity ofeach member of the protease library is measured using the desiredsubstrate sequence from the VEGF or VEGFR target protein. As a result,proteases with the highest cleavage activity with regard to the desiredsubstrate sequence are detected.

In another aspect of this embodiment, the number of mutations made tothe protease scaffold is 1, 2-5 (e.g. 2, 3, 4 or 5), 5-10 (e.g. 5, 6, 7,8, 9 or 10), or 10-20 (e.g. 10, 11, 12, 13, 14, 15, 16, 17, 18, 19 or20). In a preferred embodiment, the mutation(s) confer increasedsubstrate specificity. In a specific embodiment, the mutation(s) arepositioned in the scaffold in at least one of the S1, S2, S3 and S4sites. In certain aspects of this embodiment, the activity of the muteinprotease is increased by at least 10-fold, 100-fold, or 1000-fold overthe activity of the wild type protease. In related aspects, the increaseis in substrate specificity.

In another embodiment of the invention, the members of a library aremade up of randomized amino acid sequences, and the cleavage activity ofeach member of the library by the protease is measured. This type oflibrary is referred to herein as a substrate library. Substratesequences that are cleaved most efficiently by the protease aredetected. In specific aspects of this embodiment, the substrate sequencein a substrate library is 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16,17, 18, 19 or 20 amino acids long.

In another embodiment of the invention, the members of the substratelibrary are made up of randomized amino acid sequences, and the cleavageselectiveness of each member of the library by the protease is measured.Substrate sequences that are cleaved most selectively by the proteaseare detected. In specific aspects of this embodiment, the substratesequence in the substrate library is 4, 5, 6, 7, 8, 9, 10, 11, 12, 13,14, 15, 16, 17, 18, 19 or 20 amino acids long.

In one embodiment of this example, the specificity is measured byobserving how many different substrate sequences the protease cleaves ata given activity. Proteases that cleave fewer substrate sequences at agiven activity have greater specificity than those that cleave moresubstrate sequences.

In one aspect of this embodiment, the substrate sequence is a part ofVEGF or a VEGFR target protein. In a specific embodiment, the substratelibrary peptides include the VEGF or VEGFR residues of the P1, P2, P3and P4 sites. In another aspect of this embodiment, the efficiency ofcleavage by the MT-SP1 muteins of the invention of the detectedsubstrate sequence is increased by at least 2-fold, at least 5-fold, atleast 10-fold, at least 100-fold, or at least 1000-fold over thecleavage activity of wild-type MT-SP1. In another aspect of thisembodiment, the sequence specificity of the MT-SP1 muteins of theinvention in cleaving the substrate sequence is increased by at least2-fold, at least 5-fold, at least 10-fold, at least 100-fold, or atleast 1000-fold over the cleavage activity of the MT-SP1 muteins of theinvention on other members of the substrate library. Profiling of wildtype and mutein target specificity may be done by positional scanningsubstrate combinatorial libraries (PSSCL), as described in PCTpublication WO 01/94332, incorporated herein by reference.

In yet another embodiment, the invention provides a method for treatinga patient having a VEGF or VEGFR-related pathology, such as cancer,macular degeneration, inflammation and diabetes. The method involvesadministering to the patient a protease that cleaves VEGF or a VEGFRprotein, so that cleaving the VEGF or VEGFR treats the pathology. In arelated embodiment, the treatment of cancer by administration of anengineered protease is in combination with treatment with at least oneother anti-cancer agent. In one aspect of this embodiment, the proteaseis an MT-SP1 mutein. In another aspect of this embodiment, the proteaseis wild-type MT-SP1.

The patient having a pathology, e.g. the patient treated by the methodsof this invention, is a mammal, or more particularly, a human.

Unless otherwise defined, all technical and scientific terms used hereinhave the same meaning as commonly understood by one of ordinary skill inthe art to which this invention pertains. Although methods and materialssimilar or equivalent to those described herein can be used in thepractice or testing of the present invention, suitable methods andmaterials are described below. All publications, patent applications,patents, and other references mentioned herein are incorporated byreference in their entirety. In the case of conflict, the presentspecification, including definitions, controls. In addition, thematerials, methods, and examples are illustrative only and are notintended to be limiting.

Other features and advantages of the invention will be apparent from thefollowing detailed description and claims.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 is a photomicrograph of a SDS PAGE gel showing bands of MT-SP1purified by a one-column purification procedure and then re-foldedthrough successive dialysis steps. MT-SP1 variants were expressed inbacteria and purified from inclusion bodies. Each protease retains highcatalytic activity and is >99% pure, and thus are appropriate forcrystallographic studies.

FIG. 2A-H are graphical representations of PSSCL profiles of wild typeMT-SP1 and six variants. The MT-SP1 profile (FIG. 2A) shows that itsspecificity is somewhat broad, such that a variety of amino acids willbe accepted in the P4 and P3 positions in addition to Arg or Lys. FIGS.2B-H are a graphic depiction of PSSCL profiles of MT-SP1 muteins CB18(FIG. 2B), CB38 (FIG. 2C), CB159 (FIG. 2D), CB83 (FIG. 2E), CB155 (FIG.2F), CB151 (FIG. 2G), and CB152 (FIG. 2H), showing narrowed specificityprofiles. The activity is represented in relative fluorescence unitsalong the y-axis by dividing each amino acid activity by the activity ofthe best amino acid within each sublibrary.

FIG. 3 is a photograph of a protein gel showing VEGFR2-Fc is efficientlycleaved by wild-type and muteins of MT-SP1.

FIGS. 4A, 4B and 4C are graphical depictions of the PSSCL substratespecificity profile at P2, P3 and P4, respectively, of human MT-SP1 in aP1-Lys fixed library. The library format for each extended position islisted above the profile. The activity is represented in pM/sec on they-axis for each amino acid along the x-axis.

FIG. 5 is a graphical representation of trypsin and MT-SP1 proteaseactivity over time in the presence of increasing levels of serum.

FIG. 6 is a graphical representation of the specificity constants forMT-SP1 and the muteins CB18, CB38, CB83, CB151, CB152, CB155 and CB159on the tetrapeptide synthetic substrates Ac-RQAR-AMC and Ac-RRVR-AMC.The variants are shown along the x-axis while specificity constants areshown along the y-axis.

FIG. 7A is a graphical representation of the amount of proliferation ofendothelial cells treated with increased concentrations of MT-SP1 andthe muteins CB18, CB83 and CB152. FIG. 7B is a photograph of a westernblot showing the cleavage of VEGFR2 in HUVEC cells in the presence ofMT-SP1, CB18 and CB83, respectively. FIG. 7C is a graphicalrepresentation of the amount of soluble extracellular VEGFR2 released byHUVECs upon treatment with MT-SP1, CB18 and CB83.

FIG. 8 is a graphical representation of the maximum dose of MT-SP1, CB18and CB152 that can be tolerated by mice.

FIG. 9 is a graphical representation of the extent of inhibition ofneovascularization by a dose of MT-SP1 and CB18.

FIG. 10 is a graphical representation of the inhibition of vascularpermeability by MT-SP1, CB18 and CB152 in the mouse Miles assay.

FIG. 11 is a photograph of a protein gel showing the cleavage of VEGF bywild-type MT-SP1 but not the selective variant CB 152.

DETAILED DESCRIPTION OF THE INVENTION

Serine proteases have a highly adaptable protein scaffold. Theseproteases differ over a broad range in their substrate recognitionproperties, ranging from highly specific to completely non-specific.Despite these differences in specificity, the catalytic mechanism iswell conserved, consisting of a substrate-binding pocket that correctlyregisters the scissile peptide in the active site. This large family ofproteases can be broadly divergent among members in their sequencespecificities yet highly conserved in their mechanism of catalysis. Thisis because substrate specificity is not only determined by localcontacts directly between the substrate peptide and the enzyme (firstsphere residues), but also by long range factors (second sphereresidues). Both first sphere and second sphere substrate binding effectsare determined primarily by loops between B-barrel domains. Becausethese loops are not core elements of the protein, the integrity of thefold is maintained while loop variants with novel substratespecificities can be selected during the course of evolution to fulfillnecessary metabolic or regulatory niches at the molecular level.

Laboratory experiments support the theory that the serine proteases arehighly adaptable enzymatic scaffolds. For instance, virtually everyaspect of subtilisin has been re-engineered, including the enzyme'ssubstrate specificity, thermostability, pH profile, catalyticefficiency, oxidative stability, and catalytic function.

To date, there have been a number of attempts to alter substratespecificity in proteases using structure-guided rational design. Onenotable example came from the laboratory of Wells and coworkers. See,Ballinger et al., Biochemistry. 1996 Oct. 22; 35 (42): 13579-85. Usingsubtilisin, an enzyme with low specificity for hydrophobic residues atthe P1 position, the authors of this reference managed to alter itsspecificity for tribasic residues radically by making 3 point mutationsin the substrate binding pocket. The resulting mutant had over a1000-fold specificity for tribasic substrates versus the originalhydrophobic substrate. In total, studies on changing the specificity ofproteases suggest it is possible to alter substrate specificityradically. This invention discloses specific muteins of the serineprotease MT-SP1 having altered target specificity and methods for usingthem to treat disease.

DEFINITION OF TERMS

Prior to setting forth the invention in detail, certain terms usedherein will be defined.

The term “allelic variant” denotes any of two or more alternative formsof a gene occupying the same chromosomal locus. Allelic variation arisesnaturally through mutation, and may result in phenotypic polymorphismwithin populations. Gene mutations can be silent (no change in theencoded polypeptide) or may encode polypeptides having altered aminoacid sequence. The term “allelic variant” is also used herein to denotea protein encoded by an allelic variant of a gene.

The term “complements of polynucleotide molecules” denotespolynucleotide molecules having a complementary base sequence andreverse orientation as compared to a reference sequence. For example,the sequence 5′ ATGCACGG 3′ is complementary to 5′ CCGTGCAT 3′.

The term “degenerate nucleotide sequence” denotes a sequence ofnucleotides that includes one or more degenerate codons (as compared toa reference polynucleotide molecule that encodes a polypeptide).Degenerate codons contain different triplets of nucleotides, but encodethe same amino acid residue (i.e., GAU and GAC triplets each encodeAsp).

A “DNA construct” is a single or double stranded, linear or circular DNAmolecule that comprises segments of DNA combined and juxtaposed in amanner not found in nature. DNA constructs exist as a result of humanmanipulation, and include clones and other copies of manipulatedmolecules.

A “DNA segment” is a portion of a larger DNA molecule having specifiedattributes. For example, a DNA segment encoding a specified polypeptideis a portion of a longer DNA molecule, such as a plasmid or plasmidfragment, which, when read from the 5′ to the 3′ direction, encodes thesequence of amino acids of the specified polypeptide.

The term “expression vector” denotes a DNA construct that comprises asegment encoding a polypeptide of interest operably linked to additionalsegments that provide for its transcription in a host cell. Suchadditional segments may include promoter and terminator sequences, andmay optionally include one or more origins of replication, one or moreselectable markers, an enhancer, a polyadenylation signal, and the like.Expression vectors are generally derived from plasmid or viral DNA, ormay contain elements of both.

The term “isolated”, when applied to a polynucleotide molecule, denotesthat the polynucleotide has been removed from its natural genetic milieuand is thus free of other extraneous or unwanted coding sequences, andis in a form suitable for use within genetically engineered proteinproduction systems. Such isolated molecules are those that are separatedfrom their natural environment and include cDNA and genomic clones, aswell as synthetic polynucleotides. Isolated DNA molecules of the presentinvention may include naturally occurring 5′ and 3′ untranslated regionssuch as promoters and terminators. The identification of associatedregions will be evident to one of ordinary skill in the art (see forexample, Dynan and Tijan, Nature 316:774-78, 1985). When applied to aprotein, the term “isolated” indicates that the protein is found in acondition other than its native environment, such as apart from bloodand animal tissue. In a preferred form, the isolated protein issubstantially free of other proteins, particularly other proteins ofanimal origin. It is preferred to provide the protein in a highlypurified form, i.e., at least 90% pure, preferably greater than 95%pure, more preferably greater than 99% pure.

The term “operably linked”, when referring to DNA segments, denotes thatthe segments are arranged so that they function in concert for theirintended purposes, e.g. transcription initiates in the promoter andproceeds through the coding segment to the terminator.

The term “ortholog” denotes a polypeptide or protein obtained from onespecies that is the functional counterpart of a polypeptide or proteinfrom a different species. Sequence differences among orthologs are theresult of speciation.

The term “polynucleotide” denotes a single- or double-stranded polymerof deoxyribonucleotide or ribonucleotide bases read from the 5′ to the3′ end. Polynucleotides include RNA and DNA, and may be isolated fromnatural sources, synthesized in vitro, or prepared from a combination ofnatural and synthetic molecules. The length of a polynucleotide moleculeis given herein in terms of nucleotides (abbreviated “nt”) or base pairs(abbreviated “bp”). The term “nucleotides” is used for both single- anddouble-stranded molecules where the context permits. When the term isapplied to double-stranded molecules it is used to denote overall lengthand will be understood to be equivalent to the term “base pairs”. Itwill be recognized by those skilled in the art that the two strands of adouble-stranded polynucleotide may differ slightly in length and thatthe ends thereof may be staggered; thus all nucleotides within adouble-stranded polynucleotide molecule may not be paired. Such unpairedends will, in general, not exceed 20 nt in length.

The term “promoter” denotes a portion of a gene containing DNA sequencesthat provide for the binding of RNA polymerase and initiation oftranscription. Promoter sequences are commonly, but not always, found inthe 5′ non-coding regions of genes.

A “protease” is an enzyme that cleaves peptide bonds in peptides,polypeptides and proteins. A “protease precursor” or a “zymogen” is arelatively inactive form of the enzyme that commonly becomes activatedupon cleavage by another protease.

The term “secretory signal sequence” denotes a DNA sequence that encodesa polypeptide (a “secretory peptide”) that, as a component of a largerpolypeptide, directs the larger polypeptide through a secretory pathwayof a cell in which it is synthesized. The larger polypeptide is commonlycleaved to remove the secretory peptide during transit through thesecretory pathway.

The term “substrate sequence” denotes a sequence that is cleaved by aprotease.

The term “target protein” denotes a protein that is cleaved at itssubstrate sequence by a protease.

The term “scaffold” refers to a wild-type or existing variant proteaseto which various mutations are made. Generally, these mutations changethe specificity and activity of the scaffold. One example of an existingvariant protease is a protease existing in an organism which has beenmutated at one or more positions compared to the wild-type proteaseamino acid sequence of the species to which the organism belongs.

An “isolated” or “purified” polypeptide or protein orbiologically-active portion thereof is substantially free of cellularmaterial or other contaminating proteins from the cell or tissue sourcefrom which the protein is derived, or substantially free from chemicalprecursors or other chemicals when chemically synthesized. The language“substantially free of cellular material” includes preparations ofproteins in which the protein is separated from cellular components ofthe cells from which it is isolated or recombinantly-produced. In oneembodiment, the language “substantially free of cellular material”includes preparations of protease proteins having less than about 30%(by dry weight) of non-protease proteins (also referred to herein as a“contaminating protein”), more preferably less than about 20% ofnon-protease proteins, still more preferably less than about 10% ofnon-protease proteins, and most preferably less than about 5% ofnon-protease proteins. When the protease protein or biologically-activeportion thereof is recombinantly-produced, it is also preferablysubstantially free of culture medium, i.e., culture medium representsless than about 20%, more preferably less than about 10%, and mostpreferably less than about 5% of the volume of the protease proteinpreparation.

The language “substantially free of chemical precursors or otherchemicals” includes preparations of protease proteins in which theprotein is separated from chemical precursors or other chemicals thatare involved in the synthesis of the protein. In one embodiment, thelanguage “substantially free of chemical precursors or other chemicals”includes preparations of protease proteins having less than about 30%(by dry weight) of chemical precursors or non-protease chemicals, morepreferably less than about 20% chemical precursors or non-proteasechemicals, still more preferably less than about 10% chemical precursorsor non-protease chemicals, and most preferably less than about 5%chemical precursors or non-protease chemicals.

The term “selectiveness” or “specificity” is a ratio of efficiency ofcleavage of a targeted substrate site versus another substrate site thatis not the targeted site. As a non-limiting example, with MT-SP1, thetargeted site is RRVR (SEQ ID NO: 14) and the non-targeted site is RQAR(SEQ ID NO: 18).

The term “peptide” refers to a polypeptide of from 2 to 40 amino acidsin length.

Substrate Specificity of Therapeutically Targeted Serine Proteases

Treatment of human disease by therapeutics mostly involves employingsmall molecules or supplying proteins such as insulin or EPO forspecific alterations to cell programs. An important new class oftherapeutics being developed is a class of proteases engineered to havea new substrate specificity such that they target disease-relatedmolecules. Methods have now been developed to determine the threedimensional structures of proteases that are specificity-programmed toattack critical cell surface molecules. Structural data on engineeredproteases complexed with target-like peptides provide a framework tounderstand direct and second shell side chain interactions thatdetermine specificity. The correlation of three dimensional structureand protease activity and specificity are of academic and demonstratedlong term clinical interest. The invention moves beyond showing theimportance of second shell site alterations in the activity of aprotease with altered specificity and provides novel MT-SP1 muteins andmethods for using them to treat disease. See, e.g., Perona, et al.(1995) Biochemistry 34(5):1489-99.

The invention provides methods of use and methods for designing andtesting disease-specific proteases programmed to target proteinscritical for maintaining cancer and other diseases. These proteasesprovide an important new approach to the treatment of cancers, e.g., byimpeding tumor growth by blocking tumor angiogenesis, as well as otherdiseases, including but not limited to macular degeneration,inflammation or diabetes, in which angiogenesis plays a causative orcontributive role.

The invention also provides methods of use and methods for designing andtesting target-specific proteases programmed to target VEGF and VEGFRwhich are critical for maintaining cancer and other diseases. Theseproteases provide an important new approach to the treatment of cancers,e.g., by impeding tumor growth by blocking tumor angiogenesis, as wellas other diseases, including but not limited to macular degeneration,inflammation or diabetes, in which angiogenesis plays a causative orcontributive role.

The invention also provides methods of use and methods for designing andtesting angiogenesis-specific proteases programmed to target proteinscritical for modulating apoptosis. These proteases provide an importantnew approach to the treatment of cancers, e.g., by impeding tumor growthby blocking tumor angiogenesis, as well as other diseases, including butnot limited to macular degeneration, inflammation or diabetes, in whichangiogenesis plays a causative or contributive role.

Methods are provided for specificity determinants in proteases, therebyallowing design of proteases for disabling proteins critical formaintaining cancer or inflammation or progressing macular degenerationor diabetes. A combination of structure-based mutagenesis and screeningare used to design the targeted proteases. Engineering proteasestargeted to attack disease-related proteins represents an entirely newsector in the biotechnology industry. Methods are also provided forcreating selective proteases as a new therapeutic modality in humandisease. Development and proof of concept experiments in animal modelsof disease provide an understanding of protease substrate selectivityand recognition in this class of enzymes and provide useful informationfor the dosing and administration of the proteases of the invention forthe treatment of human disease.

This disclosure provides protease therapeutic agents, methods for theirproduction and reagents useful therewith. The methods use proteases toaddress growing health concerns such as cardiovascular disease,inflammatory disorders and cancer.

In one embodiment, the invention characterizes the three-dimensionalstructures, activity and specificity of serine proteases with novelextended substrate specificity that are targeted to the vascularendothelial growth factor receptor 2 (VEGF-R2). These proteases weredeveloped using protein engineering and selected using unique andpowerful protease profiling technology. Built from a MT-SP1 wild-typeprotease scaffold, they represent a new therapeutic modality in thetreatment of cancer.

Signaling by vascular endothelial growth factor (VEGF) and its receptorsis implicated in pathological angiogenesis and the rapid development oftumor vasculature in cancer. Drugs that block this signaling pathwayprevent the growth and maintenance of tumor blood supply, which leads tothe systematic death of the tumor. The recent success of the anti-VEGFantibody AVASTIN™ in patients with metastatic colon cancer has validatedVEGF as a target for anti-angiogenic therapy of cancer. Despite theseencouraging results, tumor progression has still occurred in anti-VEGFtreatment.

The mechanism shows that the AVASTIN™ (bevacizumab) antibody binds VEGFand prevents it from binding to its receptor. Knock-down experimentsshow that blocking VEGF function blocks angiogenesis. Thus, theinhibition of angiogenic signaling through VEGFR-2 represents anunderdeveloped therapeutic area ideal for the development of engineeredproteases with novel targeting.

Treatment with a protease that specifically cleaves and inactivates thesignaling of the VEGF/VEGFR-2 complex will attenuate the angiogenicsignal and create a pool of soluble receptor that lowers free VEGFlevels. Variant proteases have an in vitro specificity that recognizes acritical region of the VEGF receptor, which is, in one embodiment, theFlk-1/KDR stalk, over a six amino acid region. Due to their catalyticnature and smaller size, engineered proteases provide a new therapeutictreatment with advantages over competing targeted binding proteins. Theadvantages are: better tumor penetration, better target saturation,higher effectiveness, and potentially lower dosing. Notably, becausethey bind, hydrolyze, and release, a single protease could cleave andinactivate hundreds to thousands of substrate VEGF receptors, offeringsubstantial therapeutic amplification. Further, wild-type MT-SP1 alsocleaves VEGFR, and is also used according to the invention to cleaveVEGFR.

VEGF-R2 and Angiogenic Pathology

Vascular endothelial growth factor (VEGF) is a cytokine that binds andsignals through a specific cell surface receptor (VEGFR) to regulateangiogenesis, the process in which new blood vessels are generated fromexisting vasculature. Pathological angiogenesis describes the increasedvascularization associated with disease and includes events such as thegrowth of solid tumors [McMahon, Oncologist. 2000; 5 Suppl 1:3-10],macular degeneration, and diabetes. In cancer, solid tumors require anever-increasing blood supply for growth and metastasis. Hypoxia oroncogenic mutation increases the levels of VEGF and VEGFR mRNA in thetumor and surrounding stromal cells leading to the extension of existingvessels and formation of a new vascular network. In wet maculardegeneration, abnormal blood vessel growth forms beneath the macula.These vessels leak blood and fluid into the macula damagingphotoreceptor cells. In diabetes, a lack of blood to the eyes can alsolead to blindness. VEGF stimulation of capillary growth around the eyeleads to disordered vessels which do not function properly.

Three tyrosine kinase family receptors of VEGF have been identified(VEGF-R-1/Flt-1, VEGF-R-2/Flk-1/KDR, VEGF-R-3/Flt-4). KDR (the mousehomolog is Flk-1) is a high affinity receptor of VEGF with a K_(d) of400-800 pM [Waltenberger, J Biol. Chem. 1994 Oct. 28; 269 (43):26988-95]expressed exclusively on endothelial cells. VEGF and KDR association hasbeen identified as a key endothelial cell-specific signaling pathwayrequired for pathological angiogenesis [Kim, Nature. 1993 Apr. 29; 362(6423):841-4; Millauer, Nature. 1994 Feb. 10; 367 (6463):576-9; Yoshiji,Hepatology. 1999 November; 30 (5): 1179-86]. Dimerization of thereceptor upon ligand binding causes autophosphorylation of thecytoplasmic domains, and recruitment of binding partners that propagatesignaling throughout the cytoplasm and into the nucleus to change thecell growth programs. Treatment of tumors with a soluble VEGF-R2inhibits tumor growth [Lin, Cell Growth Differ. 1998 January; 9(1):49-58], and chemical inhibition of phosphorylation causes tumorscells to become apoptotic [Shaheen, Cancer Res. 1999 Nov. 1; 59(21):5412-6].

Therapies targeting the VEGF receptors and Flk-1/KDR specifically haveinhibited pathological angiogenesis and shown reduction of tumor size inmultiple mouse models of human and mouse solid tumors [Prewett, CancerRes. 1999 Oct. 15; 59 (20):5209-18; Fong, Neoplasia. 1999 April; 1(1):31-41. Erratum in: Neoplasia 1999 June; 1 (2): 183] alone and incombination with cytotoxic therapies [Klement, J Clin Invest. 2000April; 105 (8):R15-24]. Studies with small molecule inhibitors andantibodies validate the VEGF receptor family as a potentanti-angiogenesis target, but more effective therapeutics are stillneeded.

VEGFR is composed of an extracellular region of seven immunoglobin(Ig)-like domains, a transmembrane region, and two cytoplasmic tyrosinekinase domains. The first three Ig-like domains have been shown toregulate ligand binding, while domains 4 through 7 have a role ininhibiting correct dimerization and signaling in the absence of ligand.As a target for selective proteolysis by engineered proteases, it hasthe following promising target characteristics:

-   -   a labile region of amino acids accessible to proteolysis;    -   high sequence identity between the human, rat and mouse species;    -   down regulation of signaling upon cleavage; and    -   proteolytic generation of soluble receptors able to        non-productively bind ligand.

Several regions of VEGF-R2 are available for specific proteolysisincluding the stalk region before the transmembrane region andunstructured loops between Ig-like domains.

MT-SP1 Proteases

The present invention provides methods for generating and screeningMT-SP1 proteases to cleave target proteins at a given substrate sequenceas well as particular muteins and methods for using them to treatdisease. Proteases are protein-degrading enzymes that recognize an aminoacid or an amino acid substrate sequence within a target protein. Uponrecognition of the substrate sequence, proteases catalyze the hydrolysisor cleavage of a peptide bond within a target protein. Such hydrolysisof the target protein can inactivate it, depending on the location ofpeptide bond within the context of the full-length sequence of thetarget sequence. The specificity of MT-SP1 proteases can be alteredthrough protein engineering. If a protease is engineered to recognize asubstrate sequence within a target protein or proteins (i) that wouldalter the function i.e. by inactivation of the target protein(s) uponcatalysis of peptide bond hydrolysis, and (ii) the target protein(s) isa point of molecular intervention for a particular disease or diseases,then the engineered protease has a therapeutic effect via aproteolysis-mediated inactivation event. In particular, MT-SP1 proteasescan be engineered to cleave specific target receptors between theirtransmembrane and cytokine or growth factor binding domains. The stalkregions that function to tether protein receptors to the surface of acell or loop regions are thereby disconnected from the globular domainsin a polypeptide chain.

In one embodiment, the target protein to be cleaved by MT-SP1 proteasesis involved with a pathology, where cleaving the target protein at agiven substrate sequence serves as a treatment for the pathology.

The protease cleaves cell surface molecules that are responsible formodulation of angiogenesis. Where the cell surface molecule is a VEGFRsignaling in tumor angiogenesis, cleavage prevents the spread of cancer.For example, cleavage of a cell surface domain from a VEGFR molecule caninactivate its ability to transmit extracellular signals, especiallycell proliferation signals. Without angiogenesis to feed the tumor,cancer cells often cannot proliferate. In one embodiment, a MT-SP1protease of the invention is therefore used to treat cancer. Also,cleavage of VEGFR can be used to modulate angiogenesis in otherpathologies, such as macular degeneration, inflammation and diabetes. Inone embodiment, cleaving a target VEGFR protein involved in cell cycleprogression inactivates the ability of the protein to allow the cellcycle to go forward. Without the progression of the cell cycle, cancercells cannot proliferate. Therefore, the MT-SP1 proteases of theinvention which cleave VEGF or VEGFR are useful in the treatment ofcancer and other cell cycle dependent pathologies.

The protease also cleaves soluble proteins that are responsible fortumorigenicity. Cleaving VEGF prevents signaling through the VEGFreceptor and decreases angiogenesis, thus decreasing disease in whichangiogenesis plays a role, such as cancer, macular degeneration,inflammation and diabetes. Further, VEGF signaling is responsible forthe modulation of the cell cycle in certain cell types. Therefore, theMT-SP1 proteases of the invention which cleave VEGF are useful in thetreatment of cancer and other cell cycle dependent pathologies.

In some embodiments, the engineered MT-SP1 protease is designed tocleave one or more of the target proteins in Table 1, therebyinactivating the activity of the protein. The MT-SP1 protease can beused to treat a pathology associated with that protein, by inactivatingit.

TABLE 1 Protease Targets Target Indication Molecule class VEGF CancerCytokine VEGFR-1/Flt-1 Cancer Receptor VEGFR-2/KDR Cancer ReceptorVEGFR-3/Flt-4 Cancer Receptor

The protease scaffold is the MT-SP1 protein disclosed below in Table 2.

TABLE 2 Protease Scaffolds Code Name Gene Link Locus S01.087membrane-type serine protease MT-SP1 84000 11q23

The wild type MT-SP1 polypeptide of SEQ ID NO:1 is provided in Table 3,and is designated as TADG-15.

TABLE 3 Wild-type MT-SP1 polypeptide (SEQ ID NO: 1)1                                                   50 TADG-15MGSDRARKGG GGPKDFGAGL KYNSRHEKVN GLEEGVEFLP VNNVKKVEKH (SEQ ID NO: 1)51                                                 100 TADG-15GPGRWVVLAA VLIGLLLVLL GIGFLVWHLQ YRDVRVQKVF NGYMRITNEN101                                                150 TADG-15FVDAYENSNS TEFVSLASKV KDALKLLYSG VPFLGPYHKE SAVTAFSEGS151                                                200 TADG-15VIAYYWSEFS IPQHLVEEAE RVMAEERVVM LPPRARSLKS FVVTSVVAFP201                                                250 TADG-15TDSKTVQRTQ DNSCSFGLHA RGVELMRFTT PGFPDSPYPA HARCQWALRG251                                                300 TADG-15DADSVLSLTF RSFDLASCDE RGSDLVTVYN TLSPMEPHAL VQLCGTYPPS301                                                350 TADG-15YNLTFHSSQN VLLITLITNT ERRHPGFEAT FFQLPRMSSC GGRLRKAQGT351                                                400 TADG-15FNSPYYPGHY PPNIDCTWNI EVPNNQHVKV SFKFFYLLEP GVPAGTCPKD401                                                450 TADG-15YVEINGEKYC GERSQFVVTS NSNKITVRFH SDQSYTDTGF LAEYLSYDSS451                                                500 TADG-15DPCPGQFTCR TGRCIRKELR CDGWADCTDH SDELNCSCDA GHQFTCKNKF501                                                550 TADG-15CKPLFWVCDS VNDCGDNSDE QGCSCPAQTF RCSNGKCLSK SQQCNGKDDC551                                                600 TADG-15GDGSDEASCP KVNVVTCTKH TYRCLNGLCL SKGNPECDGK EDCSDGSDEK601                                                650 TADG-15DCDCGLRSFT RQARVVGGTD ADEGEWPWQV SLHALGQGHI CGASLISPNW651                                                700 TADG-15LVSAAHCYID DRGFRYSDPT QWTAFLGLHD QSQRSAPGVQ ERRLKRIISH701                                                750 TADG-15PFFNDFTFDY DIALLELEKP AEYSSMVRPI CLPDASHVFP AGKAIWVTGW751                                                800 TADG-15GHTQYGGTGA LILQKGEIRV INQTTCENLL PQQITPRMNC VGFLSGGVDS801                                                850 TADG-15CQGDSGGPLS SVEADGRIFQ AGVVSWGDGC AQRNKPGVYT RLPLFRDWIK TADG-15 ENTGV

A ClustalW alignment is provided in Table 4, comparing the wild typeMT-SP1 polypeptide of SEQ ID NO:1, designated as TADG-15, to the MT-SP1protease domain of SEQ ID NO:2. MT-SP1 protease domain residues targetedfor mutagenesis are shown in bold. The MT-SP1 protease domain iscomposed of a pro-region and a catalytic domain. The catalyticallyactivity portion of the sequence begins after the autoactivation site:RQAR (SEQ ID NO: 18) with the sequence VVGG (SEQ ID NO: 6) (underlined).

TABLE 4 ClustalW of MT-SP1 Protease Domain PileUp   MSF: 855  Type: P   Check: 4738  .. Name: MTSP_protease_domain      Len: 855     Check: 8683  Weight: 0 Name: TADG-15      Len: 855     Check: 6055  Weight: 0 //1                                                   50MTSP_protease_domain.......... .......... .......... .......... .......... (SEQ ID NO: 2)             TADG-15MGSDRARKGG GGPKDFGAGL KYNSRHEKVN GLEEGVEFLP VNNVKKVEKH (SEQ ID NO: 1)51                                                 100MTSP_protease_domain.......... .......... .......... .......... ..........             TADG-15GPGRWVVLAA VLIGLLLVLL GIGFLVWHLQ YRDVRVQKVF NGYMRITNEN101                                                150MTSP_protease_domain.......... .......... .......... .......... ..........             TADG-15FVDAYENSNS TEFVSLASKV KDALKLLYSG VPFLGPYHKE SAVTAFSEGS151                                                200MTSP_protease_domain.......... .......... .......... .......... ..........             TADG-15VIAYYWSEFS IPQHLVEEAE RVMAEERVVM LPPRARSLKS FVVTSVVAFP201                                                250MTSP_protease_domain.......... .......... .......... .......... ..........             TADG-15TDSKTVQRTQ DNSCSFGLHA RGVELMRFIT PGFPDSPYPA HARCQWALRG251                                                300MTSP_protease_domain.......... .......... .......... .......... ..........             TADG-15DADSVLSLTF RSFDLASCDE RGSDLVTVYN TLSPMEPHAL VQLCGTYPPS301                                                350MTSP_protease_domain.......... .......... .......... .......... ..........             TADG-15YNLTFHSSQN VLLITLITNT ERRHPGFEAT FFQLPRMSSC GGRLRKAQGT351                                                400MTSP_protease_domain.......... .......... .......... .......... ..........             TADG-15FNSPYYPGHY PPNIDCTWNI EVPNNQHVKV SFKFFYLLEP GVPAGTCPKD401                                                450MTSP_protease_domain.......... .......... .......... .......... ..........             TADG-15YVEINGEKYC GERSQFVVTS NSNKITVRFH SDQSYTDTGF LAEYLSYDSS451                                                500MTSP_protease_domain.......... .......... .......... .......... ..........             TADG-15DPCPGQFTCR TGRCIRKELR CDGWADCTDH SDELNCSCDA GHQFTCKNKF501                                                550MTSP_protease_domain.......... .......... .......... .......... ..........             TADG-15CKPLFWVCDS VNDCGDNSDE QGCSCPAQTF RCSNGKCLSK SQQCNGKDDC551                                                600MTSP_protease_domain.......... .......... .......... .......... .......DEK             TADG-15GDGSDEASCP KVNVVTCTKH TYRCLNGLCL SKGNPECDGK EDCSDGSDEK601                                                650MTSP_protease_domainDCDCGLRSFT RQARVVGGTD ADEGEWPWQV SLHALGQGHI CGASLISPNW             TADG-15DCDCGLRSFT RQARVVGGTD ADEGEWPWQV SLHALGQGHI CGASLISPNW651                                                700MTSP_protease_domainLVSAAHCYID DRGFRYSDPT QWTAFLGLHD QSQRSAPGVQ ERRLKRIISH             TADG-15LVSAAHCYID DRGFRYSDPT QWTAFLGLHD QSQRSAPGVQ ERRLKRIISH701                                                750MTSP_protease_domainPFFNDFTFDY DIALLELEKP AEYSSMVRPI CLPDASHVFP AGKAIWVTGW             TADG-15PFFNDFTFDY DIALLELEKP AEYSSMVRPI CLPDASHVFP AGKAIWVTGW751                                                800MTSP_protease_domainGHTQYGGTGA LILQKGEIRV INQTTCENLL PQQITPRMMC VGFLSGGVDS             TADG-15GHTQYGGTGA LILQKGEIRV INQTTCENLL PQQITPRMMC VGFLSGGVDS801                                                850MTSP_protease_domainCQGDSGGPLS SVEADGRIFQ AGVVSWGDGC AQRNKPGVYT RLPLFRDWIK             TADG-15CQGDSGGPLS SVEADGRIFQ AGVVSWGDGC AQRNKPGVYT RLPLFRDWIK 851MTSP_protease_domain ENTGV              TADG-15 ENTGV

A ClustalW alignment is provided in Table 5, comparing the wild typeMT-SP1 protease domain of SEQ ID NO:2 with human chymotrypsin. MT-SP1protease domain residues targeted form mutagenesis are numberedaccording to chymotrypsin.

TABLE 5ClustalW alignment of human chymotrypsin and MT-SP1 protease domains16           30 31           45 46           60 61           66Chymotrypsin BIVNGEDAVPGSWPWQ VSLQDKTGFHFCGGS LISEDWVVTAAHCGV ---------RTSDVV(SEQ ID NO: 3) MTSP_protease_domainVVGGTDADEGEWPWQ VSLHALGQGHICGAS LISPNWLVSAAHCYI DDRGFRYSDPTQWTA(SEQ ID NO: 2)67           80 81           95 96          110 111         125Chymotrypsin BVAGEFDQGS-DEENI QVLKIAKVFKNPKFS ILTVNNDITLLKLAT PARFSQTVSAVCLPSMTSP_protease_domainFLGLHDQSQRSAPGV QERRLKRIISHPFFN DFTFDYDIALLELEK PAEYSSMVRPICLPD126         140 141         155 156         170 171         184Chymotrypsin BADDDFPAGTLCATTG WGKTKYNANKTPDKL QQAALPLLSNAECKK SWGRRITDVMICAG-MTSP_protease_domainASHVFPAGKAIWVTG WGHTQYGG-TGALIL QKGEIRVINQTTCEN LLPQQITPRMMCVGF185         198 199         212 213         226 227         240Chymotrypsin B-ASGVSSCMGDSGGP L-VCQKDGAWTLVGI VSWGSDTCSTSS-PG VYARVTKLIPWVQKIMTSP_protease_domainLSGGVDSCQGDSGGP LSSVEADGRIFQAGV VSWGDG-CAQRNKPG VYTRLPLFRDWIKEN 241Chymotrypsin B LAAN MTSP_protease_domina TGV-

A DNA sequence is provided in Table 6 which encodes the catalytic domain(SEQ ID NO:2) of wild type MT-SP1 protease domain as contained withinthe pQE cloning vector.

TABLE 6 The DNA sequence of the catalytic domain of wild type MT-SP1.gtt gtt ggg ggc acg gat gcg gat gag ggc gag tgg ccc tgg cag gta agc ctg cat gct(SEQ ID NO: 4)ctg ggc cag ggc cac atc tgc ggt gct tcc ctc atc tct ccc aac tgg ctg gtc tct gccgca cac tgc tac atc gat gac aga gga ttc agg tac tca gac ccc acg cag tgg acg gccttc ctg ggc ttg cac gac cag agc cag cgc agc gcc cct ggg gtg cag gag cgc agg ctcaag cgc atc atc tcc cac ccc ttc ttc aat gac ttc acc ttc gac tat gac atc gcg ctgctg gag ctg gag aaa ccg gca gag tac agc tcc atg gtg cgg ccc atc tgc ctg ccg gacgcc tcc cat gtc ttc cct gcc ggc aag gcc atc tgg gtc acg ggc tgg gga cac acc cagtat gga ggc act ggc gcg ctg atc ctg caa aag ggt gag atc cgc gtc atc aac cag accacc tgc gag aac ctc ctg ccg cag cag atc acg ccg cgc atg atg tgc gtg ggc ttc ctcagc ggc ggc gtg gac tcc tgc cag ggt gat tcc ggg gga ccc ctg tcc agc gtg gag gcggat ggg cgg atc ttc cag gcc ggt gtg gtg agc tgg gga gac ggc tgc gct cag agg aacaag cca ggc gtg tac aca agg ctc cct ctg ttt cgg gac tgg atc aaa gag aac act ggggta tagEngineering MT-SP1 Muteins

Virtually every aspect of a protease, including MT-SP1, can bere-engineered, including the enzyme substrate sequence specificity,thermostability, pH profile, catalytic efficiency, oxidative stability,and catalytic function.

Wild-type MT-SP1 protease is used in accordance with the methods of theinvention as a scaffold for incorporating various mutations that changeits substrate specificity. Among the determinants of substrate sequencespecificity in serine proteases come from the S1-S4 positions in theactive site, where the protease is in contact with the P1-P4 residues ofthe peptide substrate sequence. In some cases, there is little (if any)interaction between the S1-S4 pockets of the active site, such that eachpocket appears to recognize and bind the corresponding residue on thepeptide substrate sequence independent of the other pockets. Thus, thespecificity determinants may be generally changed in one pocket withoutaffecting the specificity of the other pockets.

For example, a MT-SP1 protease with low specificity for a residue at aparticular binding site or for a particular sequence is altered in itsspecificity by making point mutations in the substrate sequence bindingpocket. In some cases, the resulting MT-SP1 mutein has a greater than2-fold increase in specificity at a site or for a particular sequencethan does wild-type. In another embodiment, the resulting MT-SP1 muteinhas a greater than 5-fold increase in specificity at a site or for aparticular sequence than does wild-type. In another embodiment, theresulting MT-SP1 mutein has a greater than 10-fold increase inspecificity at a site or for a particular sequence than does wild-type.In another embodiment, the resulting MT-SP1 mutein has a greater than100-fold increase in specificity at a site or for a particular sequencethan does wild-type. In another embodiment, the resulting MT-SP1 muteinhas an over 1000-fold increase in specificity at a site or for aparticular sequence than does wild-type.

One embodiment of this example, the specificity is measured by observinghow many disparate substrate sequences a mutein protease cleaves at agiven activity as compared to the number in the wild-type protease. Ifthe mutein protease cleaves fewer substrate sequences than thewild-type, then the mutein protease has greater specificity than thewild-type. A mutein that has 10 fold higher specificity than a wild-typeprotease cleaves 10 fold fewer substrate sequences than the wild-typeprotease.

Also contemplated by the invention are libraries of MT-SP1 scaffoldswith various mutations that are generated and screened using methodsknown in the art and those detailed herein. Libraries are screened toascertain the substrate sequence specificity of the members. Librariesof MT-SP1 scaffolds are tested for specificity by exposing the membersto substrate peptide sequences. The MT-SP1 member with the mutationsthat allow it to cleave the substrate sequence is identified. The MT-SP1 scaffold library is constructed with enough variety of mutation inthe scaffold such that a variety of substrate peptide sequences arecleaved by various members of the MT-SP1 scaffold library. Thus,proteases specific for any target protein can be generated.

Particular protease residues that, upon mutation, affect the activityand specificity of MT-SP1 scaffold protease are described here. MT-SP1is a serine protease. The serine proteases are members of the samefamily as chymotrypsin. In one embodiment of the invention, MT-SP1muteins with altered specificity are generated by a structure-baseddesign approach. Each protease has a series of amino acids that linesthe active site pocket and makes direct contact with the substrate.Throughout the chymotrypsin family, the backbone interaction between thesubstrate and enzyme is completely conserved, but the side chaininteractions vary considerably. The identity of the amino acids thatcomprise the S1-S4 pockets of the active site determines the substratespecificity of that particular pocket. Grafting the amino acids of oneserine protease to another of the same fold modifies the specificity ofone to the other. Scaffold residues of serine proteases are identifiedusing chymotrypsin numbering. For example, a mutation at position 99 inthe S2 pocket to a smaller amino acid confers a preference for largerhydrophobic residues in the P2 substrate position. Using this process ofselective mutagenesis, followed by substrate library screening, one cangenerate and identify proteases with novel substrate specificitiestowards proteins involved with various diseases.

The amino acids of the protease that comprise the S1-S4 pockets arethose that have side chains within 4 to 5 angstroms of the substrate.The interactions these amino acids have with the protease substrate aregenerally called “first shell” interactions because they directlycontact the substrate. There are also “second shell” and “third shell”interactions that ultimately position the first shell amino acids. Theinvention also contemplates the mutation of those amino actions whichundergo second and third shell interactions in order to change thespecificity and rate of reaction of the mutein protease of theinvention.

Chymotrypsin family members share sequence and structural homology withchymotrypsin. Based on chymotrypsin numbering, the active site residuesare Asp102, His57, and Ser 195. The linear amino acid sequence can bealigned with that of chymotrypsin and numbered according to the β sheetsof chymotrypsin. Insertions and deletions occur in the loops between thebeta sheets, but throughout the structural family, the core sheets areconserved. The serine proteases interact with a substrate in a conservedβ sheet manner. Up to 6 conserved hydrogen bonds can occur between thesubstrate and the enzyme. All serine proteases of the chymotrypsinfamily have a conserved region at their N-terminus that is necessary forcatalytic activity. It is generally IIGG, VVGG or IVGG (SEQ ID NOS: 5, 6and 7, respectively). Where the first amino acid in this quartet isnumbered according to the chymotrypsin numbering, it is given thedesignation of Ile16. This numbering does not reflect the length of theprecursor region. Also, in one embodiment, the muteins described hereinare on the rat MT-SP1 scaffold. In another embodiment, the muteinsdescribed herein are on the human scaffold. The chymotrypsin numberingand residues referred to herein apply to the rat and human MT-SP1scaffold. Both human and rat muteins can be made using the expressionsystems of the invention. MT-SP1 scaffolds isolated or cloned from otherspecies are also encompassed within this invention.

MT-SP1 Structural Determinants

Serine protease substrate recognition sites are labeled according to themethod of Schecter and Berger Biochem. Biophys. Res. Commun. 27 (1967)157-162. Labels increase in number from P1, P2, . . . Pn for thesubstrate amino acids N-terminal to the scissile bond and P1′, P2′, . .. Pn′ for the substrate amino acids C-terminal to the scissile bond. Thecorresponding substrate recognition pockets on the enzyme are labeled,Sn . . . S2, S1, S1′, S2′ . . . Sn′. Thus, P2 interacts with S2, P1 withS1, P1′ with S1′, etc. Amino acids in the MT-SP1 scaffold are numberedaccording to their alignment with the serine protease chymotrypsin. See,Blow, D. M. (1976) Acc. Chem. Res. 9, 145-152.

For serine proteases, the following amino acids in the primary sequenceare determinants of specificity: 195, 102, 57 (the catalytic triad);189, 190, 191, 192, and 226 (P1); 57, the loop between 58 and 64, and 99(P2); 192, 217, 218 (P3), the loop between Cys168 and Cys182, 215 and 97to 100 (P4). Position 189 in a serine protease is a residue buried atthe bottom of the pocket that determines the P1 specificity. To make avariant protease with an altered substrate recognition profile, theamino acids in the three-dimensional structure that contribute to thesubstrate selectivity (specificity determinants) are targeted formutagenesis. For the serine proteases, numerous structures of familymembers have defined the surface residues that contribute to extendedsubstrate specificity (Wang et al., Biochemistry 2001 Aug. 28; 40(34):10038-46; Hopfner et al., Structure Fold Des. 1999 Aug. 15; 7(8):989-96; Friedrich et al. J Biol. Chem. 2002 Jan. 18; 277 (3):2160-8;Waugh et al., Nat Struct Biol. 2000 September; 7 (9):762-5).

Structural determinants for MT-SP1 are listed in Table 7 following thenumbering of chymotrypsin. The number underneath the Cys168-Cys182 and60's loop column headings indicate the number of amino acids in the loopbetween the two amino acids. The yes/no designation under theCys191-Cys220 column heading indicates whether the disulfide bridge ispresent in this protease. These regions are variable within the familyof chymotrypsin-like serine proteases and represent structuraldeterminants in themselves.

TABLE 7 Structural determinants for MT-SP1. Scaffold Residues thatDetermine Specificity S2 S4 60's S1 Cys¹⁶⁸ S3 loop Cys¹⁹¹ 171 174 180215 Cys¹⁸² 192 218 99 57 (58–64) 189 190 226 Cys²²⁰ MT- Leu Gln Met Trp13 Gln Asp Phe His 16 Asp Ser Gly yes SP1

The positional scanning synthetic combinatorial library (PSSCL) resultsfor the P1 through P4 substrate positions of MT-SP1, chymotrypsin,trypsin and thrombin are provided in Table 8. In Table 8, “Hyd”represents any hydrophobic amino acid (i.e. glycine, alanine, valine,leucine, isoleucine, phenylalanine, tyrosine, or tryptophan). “Xxx”represents any amino acid.

TABLE 8 Substrate specificities for MT-SP1 and related proteases.Substrate Specificity P4 P3 P2 P1 MT-SP1 Arg Hyd Ser Arg Hyd Arg Thr LysChymotrypsin Xxx Xxx Val Phe Pro Val Trypsin Xxx Xxx Ala Arg Ser LysThrombin Phe Xxx Pro Arg Leu LysMT-SP1 Mutein Constructs

To change the substrate preference of a given subsite (S1-S4) for agiven amino acid, the specificity determinants that line the bindingpocket are mutated, either individually or in combination. The resultingset of protease muteins, each different member having a differentspecificity and one or more differing mutations from one another, andthe coding sequences and expression vectors producing them, constituteimportant aspects of the present invention. In one embodiment of theinvention, a saturation mutagenesis technique is used in which theresidue(s) lining the pocket is mutated to each of the 20 possible aminoacids. This can be accomplished using the Kunkle method (In: CurrentProtocols in Molecular Biology, Ausubel et al. (eds.) John Wiley andSons, Inc., Media Pa.). Briefly, a mutagenic oligonucleotide primer issynthesized that contains either NNS or NNK-randomization at the desiredcodon. The primer is annealed to the single stranded DNA template, andDNA polymerase is added to synthesize the complementary strain of thetemplate. After ligation, the double stranded DNA template istransformed into E. coli for amplification. Alternatively, single aminoacid changes are made using standard, commercially availablesite-directed mutagenesis kits such as QuikChange (Stratagene). Inanother embodiment, any method commonly known in the art for sitespecific amino acid mutation of MT-SP1 could be used to prepare a set ofMT-SP1 muteins of the invention that can be screened to identify muteinsthat cleave VEGF, a VEGFR, or another target protein.

MT-SP1 is a mosaic protein containing a transmembrane domain, two CUBdomains, four LDLR repeats, and a serine protease domain. The proteasedomain of MT-SP1 has been expressed in bacteria or yeast in milligramquantities and purified. Profiling by positional scanning substratecombinatorial libraries (PSSCL) revealed that it has trypsin-likeactivity, demonstrating a strong preference for basic residues at the P1position. The extended P2-P4 specificity of MT-SP1 is shown in Table 9.

TABLE 9 Extended P2–P4 Specificity of Wild Type MT-SP1 P4 P3 P2 P1Arg/Lys Xxx Xxx Arg/Lys or Xxx Arg/Lys Xxx Arg/Lys wherein Xxx is anyamino acid.

Thus MT-SP1 appears to have a specificity switch, wherein it accepts apositively charged residue in the P4 position or a positively chargedresidue in the P3 position. The crystal structure of the protease domainof MT-SP1 has been solved, providing a structural rationale for itssubstrate specificity profile.

To develop novel muteins useful for attenuating VEGF signaling foranti-angiogenesis therapy, MT-SP1 polypeptides are engineered to cleaveand inactivate VEGF receptor 2 (KDR) selectively. Wildtype MT-SP1protease domain (herein referred to as MT-SP1) and mutants thereof arecloned, expressed, purified, and profiled by PSSCL. See, PCT publicationWO 01/94332, incorporated by reference herein in its entirety. Wildtypeand mutant MT-SP1 are then assayed for the cleavage of purified VEGFreceptor, as further described and illustrated in the Examples below.

MT-SP1 variants that are able to cleave the purified VEGF receptor areassayed for the cleavage of the receptor on endothelial cells, whereincleavage results in abrogation of cell proliferation resulting from VEGFsignaling. See, e.g. Yilmaz et al., 2003 Biochem. Biophys. Res. Commun.306 (3): 730-736; Gerber et al., 1998 J Biol Chem. 273 (46): 30336-43.Promising variants are then tested in animal models angiogenesis andtumor growth, including the mouse micropocket corneal assay and tumorxenografts. See, e.g. Kuo et al., PNAS, 2001, 98:4605-4610.

Mutants of MT-SP1 were made by QuikChange PCR (Stratagene) according tothe manufacturer's protocol. A non-limiting listing of a variety ofresulting mutant MT-SP1 polypeptides (muteins) is provided in Table 10,and their corresponding CB numbers are provided in Table 11. The MT-SP1wild-type residues, identified using chymotrypsin numbering, areprovided in the left column, and the MT-SP1 mutants are provided in theright column. Asp60b and Arg60c are part of an insertion in MTSP notpresent in chymotrypsin. Therefore, all the residues in this loop areassigned to residue 60 with chymotrypsin numbering.

TABLE 10 MT-SP1 mutein constructs wild type MT-SP1 residue (chymotrypsinnumbering) Replacement Mutein residue Asp60b Ala, Arg, Ile, Phe Arg60cAla, Asp, Ile, Phe, Trp Phe97 Ala, Arg, Asn, Asp, Glu, Trp Phe99 Ala,Arg, Asn, Asp, Glu, Tyr, Trp, Val Tyr146 Ala, Arg, Asn, Asp, Glu, Phe,Trp Leu172 Ala, Arg, Asn, Asp, Glu, Phe Gln175 Ala, Arg, Asp, Glu, Phe,Val Met180 Ala, Arg, Glu, Tyr Gln192 Ala, Arg, Asp, Phe, Val Trp215 Arg,Asp, Ile, Phe, Tyr Asp217 Ala, Arg, Glu, Phe, Val Lys224 Ala, Asp, Phe,Val

TABLE 11 MT-SP1 muteins labeled by CB number CB0011 F97N CB0012 F97DCB0013 F97E CB0014 F99Y CB0015 F99W CB0016 Y146F CB0017 L172N CB0018L172D CB0019 L172E CB0020 Q175D CB0021 Q175E CB0022 D217A CB0023 D217VCB0024 D217F CB0031 F97A CB0032 F97W CB0033 F97R CB0034 F99N CB0035 F99DCB0036 F99E CB0037 F99A CB0038 F99V CB0039 F99R CB0040 Y146N CB0041Y146D CB0042 Y146E CB0043 Y146A CB0044 Y146W CB0045 Y146R CB0046 L172ACB0047 L172V CB0048 L172F CB0049 L172R CB0050 Q175A CB0051 Q175V CB0052Q175F CB0053 Q175R CB0054 D217E CB0055 D217R CB0056 W215F CB0057 W215YCB0058 W215I CB0059 W215D CB0060 W215R CB0061 Q192A CB0062 Q192V CB0063Q192D CB0064 Q192R CB0065 Q192F CB0066 K224A CB0067 K224F CB0068 K224VCB0069 K224D CB0070 M180E CB0071 M180Y CB0072 M180R CB0073 M180A CB0074D60bI CB0075 D60bF CB0076 D60bR CB0077 D60bA CB0078 R60cI CB0079 R60cFCB0080 R60cD CB0081 R60cA CB0082 R60cW CB0083 L172D/Q175D CB0150F99V/L172D CB0151 F99V/L172D/Q175D CB0152 F99V/K224F CB0153 F99V/M180ECB0154 F99V/Y146D CB0155 Y146D/K224F CB0156 Y146D/M180E CB0157Y146D/L172D/Q175D CB0158 F99V/Y146D/L172D/Q175D CB0159 F99I/L172D/Q175DCB0160 F99L/L172D/Q175D CB0161 F99T/L172D/Q175D CB0162 F99A/L172D/Q175DCB0173 F99I/K224F CB0174 F99L/K224F CB0175 F99T/K224F CB0176F99V/Y146D/K224F CB0177 F99I/Y146D/K224F CB0178 F99L/Y146D/K224F CB0179F99T/Y146D/K224F

In Table 11, mutations are identified using the chymotrypsin numberingsystem. Thus, W215Y means that a tryptophan at position 215 of MT-SP1according to the chymotrypsin numbering system is changed to a tyrosineat that position.

In any given embodiment, a mutated MT-SP1 polypeptide (“mutein”) maycontain a single mutation per polypeptide, or may contain two or moremutated residues per polypeptide, in any combination. Exemplaryreplacements of wild-type residues are provided in Table 10. In oneexemplary embodiment, a Leu residue at position 172 is replaced with anAsp residue, wherein the mutein is designated as L172D. In anotherexemplary embodiment, an Asp60b residue is replaced by any one of Ala,Arg, Ile or Phe. In a further exemplary embodiment a variant MT-SP1includes at least one of Y146F, L172D, Q175D and D217F, and may containtwo, three, four or more such residue replacements.

Expression And Purification of MT-SP1 Muteins

In one embodiment, the protease is expressed in an active form. Inanother embodiment, the protease is expressed in an inactive, zymogenform. In one embodiment, the protease is expressed by a heterologousexpression system such as an E. coli, Pichia pastoris, S. cerevisiae, ora baculovirus expression system. In a preferred embodiment, the proteaseis expressed in a mammalian cell culture expression system. Exemplarymammalian cell cultures are derived from rat, mouse, or preferably humancells. The protein can either be expressed in an intracellularenvironment or excreted (secreted) into the media. The protease can alsobe expressed in an in vitro expression system.

To purify variant MT-SP1 proteases, column chromatography can be used.The protease may be engineered to contain a 6-His tag for purificationon a Nickel column. Depending on the pI of the protease, a cation oranion exchange column can be used in the purification method for theprotease. Purification can also be accomplished throughimmunoabsorption, gel filtration, or any other purification method usedin the art. The protease can be stored in a low pH buffer that minimizesits catalytic activity so that it will not degrade itself. This isfurther illustrated in Example 2.

Synthesis of Libraries for Characterization of MT-SP1 Muteins

Those of skill in the art will recognize that many methods can be usedto prepare the peptides and the libraries of the invention. Suitableembodiments are further illustrated in Example 3.

Determination of Specificity Changes for MT-SP1 Muteins

Essential amino acids in the MT-SP1 muteins generated using the methodsof the present invention are identified according to procedures known inthe art, such as site-directed mutagenesis or saturation mutagenesis ofactive site residues, or disclosed herein. In one technique, residuesthat form the S1-S4 pockets that have been shown to be importantdeterminants of specificity are mutated to every possible amino acid,either alone or in combination. See, e.g., Legendre, et al., JMB (2000)296: 87-102. Substrate specificities of the resulting mutants will bedetermined using the ACC positional scanning libraries and by singlesubstrate kinetic assays. See, e.g., Harris, et al. PNAS, 2000,97:7754-7759.

Multiple amino acid substitutions are made and tested using knownmethods of mutagenesis and screening, such as those disclosed herein oralready known in the art. See, e.g., Reidhaar-Olson and Sauer 1988Science 241:53-57, or Bowie and Sauer 1989 Proc. Natl. Acad. Sci. USA86:2152-2156. Briefly, these authors disclose methods for simultaneouslyrandomizing two or more positions in a polypeptide, selecting forfunctional polypeptide, and then sequencing the mutagenized polypeptidesto determine the spectrum of allowable substitutions at each position.Other methods that can be used include phage display based methods(e.g., Legendre et al., JMB, 2000: 296:87-102; Lowman et al., Biochem.30:10832-10837, 1991; Ladner et al., U.S. Pat. No. 5,223,409; Huse, PCTPublication WO 92/06204) and region-directed mutagenesis (Derbyshire etal., Gene 46:145, 1986; Ner et al., DNA 7:127, 1988).

Mutagenesis methods as disclosed above can be combined withhigh-throughput, automated screening methods to detect activity ofcloned, mutagenized polypeptides in host cells. Mutagenized DNAmolecules that encode proteolytically active proteins or precursorsthereof are recovered from the host cells and rapidly sequenced usingmodern equipment. These methods allow the rapid determination of theimportance of individual amino acid residues in a polypeptide ofinterest, and can be applied to polypeptides of unknown structure.

In one embodiment, protease phage display is used to screen thelibraries of mutant proteases of the invention for various affinities tospecific substrate sequences as described in the art. See, e.g.,Legendre et al., JMB, 2000: 296:87-102, and Corey et al., Gene, 1993Jun. 15; 128 (1):129-34.

The invention also provides methods for detecting and quantitating anenzymatically active protease of the invention. The method includes: (a)contacting a sample with a protease, in such a manner whereby afluorogenic moiety is released from a peptide substrate sequence uponaction of the protease, thereby producing a fluorescent moiety; and (b)observing whether the sample undergoes a detectable change influorescence, the detectable change being an indication of the presenceof the enzymatically active protease in the sample.

In one embodiment, these methods are used select for an MT-SP1 muteinthat specifically cleaves a target sequence in VEGF or VEGFR, andpreferably for an enzymatically active protease. In another embodiment,these methods are used to determine the sequence specificity of anMT-SP1 mutein. Suitable methods for determining specificity of MT-SP1muteins are further illustrated in Examples 3-5.

The methods illustrated in Examples 1-5 can be repeated iteratively orin parallel to create a variant protease that has the desiredspecificity and selectivity at each of the extended binding subsites,P2, P3, and P4. In some cases, mutations in serine proteases have shownthat each of the subsites that form the active site (S1-S4) functionindependently of one another, such that modification of specificity atone subsite has little influence on specificity at adjacent subsites.Thus, engineering substrate specificity and selectivity throughout theextended binding site can be accomplished in a step-wise manner.

Mutant proteases that match the desired specificity profiles, asdetermined by substrate libraries, are then assayed using individualpeptide substrates corresponding to the desired cleavage sequence.Variant proteases are also assayed to ascertain that they will cleavethe desired sequence when presented in the context of the full-lengthprotein. The activity of the target protein is also assayed to verifythat its function has been destroyed by the cleavage event. The cleavageevent is monitored by SDS-PAGE after incubating the purified full-lengthprotein with the variant protease. In another embodiment, mutations arecombined to acquire the specificity of multiple proteases. A mutation atone residue of a scaffold, which produces specificity at one site, iscombined in the same protease with another mutation at another site onthe scaffold to make a combined specificity protease.

Any number of mutations at discrete sites on the same scaffold can beused to create a combined specificity protease. In one embodiment, theMT-SP1 scaffold comprises a polypeptide 95% identical to the amino acidsequence of wild type MT-SP1 of SEQ ID NO:1, and the polypeptide has atleast one mutation at one or more of the positions 171, 174, 180, 215,192, 218, 99, 57, 189, 190, 226, 146, 172, 175, 41, 58, 59, 60, 61, 62,63, 97, 98, 100, 102, 151, 169, 170, 171A, 173, 176, 177, 178, 179, 181,191, 195 or 224 or 217, wherein the numbering is for chymotrypsin.

These sites belong to the following S pockets:

S1′: 146, 151,

S1: 189, 190, 226, 191, 195

S2: 99, 41, 57, 58, 59, 60, 61, 62, 63, 97, 98, 100, 102

S3: 192, 218, 146

S4: 171, 174, 179, 180, 215, 99, 172, 175, 97. 98, 169, 170, 171A, 173,176, 177, 178, 181, 224, 217

In an exemplary embodiment, the mutein is L172D comprising leucinereplaced with aspartic acid at position 172. In another embodiment, themutein is Y146F comprising tyrosine replaced with phenylalanine atposition 146. In a another embodiment, the mutein is Q175D comprisingglutamine replaced with aspartic acid at position 175. In anotherembodiment, the mutein is D217F comprising aspartic acid replaced withphenylalanine at position 217. In one embodiment, at least one residueis replaced as compared to the MT-SP1 wild type polypeptide sequence ofSEQ ID NO:1. Further nonlimiting contemplated MT-SP1 muteins areprovided herein.

Proteins targeted for cleavage and inactivation can be identified by thefollowing criteria: 1) the protein is involved in pathology; 2) there isstrong evidence the protein is the critical point of intervention fortreating the pathology; 3) proteolytic cleavage of the protein willlikely destroy its function. By these criteria, VEGF and the VEGFRs areexcellent targets for protease-mediated therapies of the invention.Cleavage sites within target proteins are identified by the followingcriteria: 1) they are located on the exposed surface of the protein; 2)they are located in regions that are devoid of secondary structure (i.e.not in β sheets or a helices), as determined by atomic structure orstructure prediction algorithms (these regions tend to be loops on thesurface of proteins or stalks on cell surface receptors); or 3) they arelocated at sites that are likely to inactivate the protein, based on itsknown function. Cleavage sequences are e.g., four residues in length tomatch the extended substrate specificity of many serine proteases, butcan be longer or shorter.

In one embodiment of the invention, target protein-assisted catalysis isused to generate proteases specific for a target VEGF or VEGFR protein.A single mutation in the substrate sequence binding site of the proteasecan alter its specificity and cause it to have a change in substratesequence specificity. Thus, substrate sequence specificity can bealtered using one or only a small number of mutations.

Using the methods disclosed above, one of ordinary skill in the art canidentify and/or prepare a variety of polypeptides that are substantiallyhomologous to a protease scaffold or allelic variants thereof and retainthe proteolysis activity of the wild-type protein scaffold but vary fromit in specificity. In one embodiment, these polypeptides are based onthe scaffold amino acid sequence of MT-SP1. Such polypeptides mayoptionally include a targeting moiety comprising additional amino acidresidues that form an independently folding binding domain. Such domainsinclude, for example, an extracellular ligand-binding domain (e.g., oneor more fibronectin type III domains) of a cytokine receptor;immunoglobulin domains; DNA binding domains (see, e.g., He et al.,Nature 378:92-96, 1995); affinity tags; and the like. Such polypeptidesmay also include additional polypeptide segments as generally disclosedabove.

Protease Polypeptides

The protease muteins and protease libraries of the invention includepolypeptides having an amino acid sequence of one or more of theproteases described herein. The invention also provides mutant orvariant proteases that, relative to MT-SP1, has residues different fromthe corresponding residues of MT-SP1, while still maintaining itsprotease activity and physiological functions, and functional fragmentsthereof. In a preferred embodiment, the mutations in the MT-SP1 muteinsof the invention occur in the S1-S4 regions of the protease as detailedherein.

In general, a protease variant that preserves protease-like functionincludes any variant in which residues at a particular position in thesequence have been substituted by other amino acids, and further includevariants produced by, relative to the wild-type or parent proteinsequence, inserting an additional residue or residues between tworesidues of the parent protein as well as by deleting one or moreresidues from the parent sequence. Any amino acid substitution,insertion, or deletion is contemplated by the methods, muteins, andmutein libraries of the invention. In favorable circumstances, thesubstitution is a conservative substitution, as described above.

One aspect of the invention pertains to isolated proteases, andbiologically-active portions thereof, as well as derivatives, fragments,analogs or homologs thereof. Also provided are polypeptide fragmentssuitable for use as immunogens to raise anti-protease antibodies. In oneembodiment, proteases of the invention are produced by recombinant DNAtechniques. As an alternative to recombinant expression, a proteaseprotein or polypeptide can be synthesized chemically using standardpeptide synthesis techniques, as described above.

Biologically-active portions of protease proteins include peptidescomprising amino acid sequences homologous to or derived from the aminoacid sequences of the full-length protease proteins, but with feweramino acids than the full-length protease proteins, and that exhibit atleast one activity of the full-length protease protein. Typically,biologically-active portions comprise a domain or motif with at leastone activity of the protease protein. A biologically-active portion of aprotease protein is a polypeptide which is, for example, 10, 25, 50, 60,70, 80, 90, 100, 110, 120, 130, 140, 150, 160, 170, 180, 190, 200, 210,220, 230, 240, 250, 260, 270, 280, 290, 300 or more amino acid residuesin length, and increasing in amino acid length in whole integers of one(1), up to a length of 855 amino acids, wherein wild-type full lengthMT-SP1 is considered to be 855 amino acids in length (SEQ ID NO:1), andmature is less than 855 aa in length. In general, a “fragment” or a“portion” of a polypeptide contains at least one less amino acid residuethan the full length polypeptide. The one or more deleted amino acidsmay be removed from the N-terminus, the C-terminus, or an internalportion.

Moreover, other biologically-active portions of a protein, from whichother regions of the protein have been deleted, can be prepared byrecombinant techniques and evaluated for one or more of the functionalactivities of a native protease.

In one embodiment, the protease has an amino acid sequence of MT-SP1 orone of the mutants of the MT-SP1 scaffold. Thus, the protease protein issubstantially homologous to MT-SP1 or one of its muteins, and retainsthe functional activity of MT-SP1, yet differs in amino acid sequencedue to natural allelic variation or mutagenesis, and may differ inspecificity, as described herein. Representative MT-SP1 muteins aredisclosed in Tables 10 and 11 herein.

Determining Homology Between Two or More Sequences

To determine the percent homology of two amino acid sequences or of twonucleic acids, the sequences are aligned for optimal comparison purposes(e.g., gaps can be introduced in the sequence of a first amino acid ornucleic acid sequence for optimal alignment with a second amino ornucleic acid sequence). The amino acid residues or nucleotides atcorresponding amino acid positions or nucleotide positions are thencompared. When a position in the first sequence is occupied by the sameamino acid residue or nucleotide as the corresponding position in thesecond sequence, then the molecules are homologous at that position(i.e., as used herein amino acid or nucleic acid “homology” isequivalent to amino acid or nucleic acid “identity”).

The nucleic acid or amino acid sequence homology may be determined asthe degree of identity between two sequences. The homology may bedetermined using computer programs known in the art, such as GAPsoftware provided in the GCG program package. See, Needleman and Wunsch,1970. J Mol Biol 48: 443-453. Using GCG GAP software with the followingsettings for nucleic acid sequence comparison: GAP creation penalty of5.0 and GAP extension penalty of 0.3, the coding region of the analogousnucleic acid sequences referred to above exhibits a degree of identitypreferably of at least 70%, 75%, 80%, 85%, 90%, 95%, 98%, or 99%.

The term “sequence identity” refers to the degree to which twopolynucleotide or polypeptide sequences are identical on aresidue-by-residue basis over a particular region of comparison. Theterm “percentage of sequence identity” is calculated by comparing twooptimally aligned sequences over that region of comparison, determiningthe number of positions at which the identical nucleic acid base (e.g.,A, T, C, G, U, or I, in the case of nucleic acids) occurs in bothsequences to yield the number of matched positions, dividing the numberof matched positions by the total number of positions in the region ofcomparison (i.e., the window size), and multiplying the result by 100 toyield the percentage of sequence identity. The term “substantialidentity” as used herein denotes a characteristic of a polynucleotidesequence, wherein the polynucleotide comprises a sequence that has atleast 80 percent sequence identity, preferably at least 85 percentidentity and often 90 to 95 percent sequence identity, more usually atleast 99 percent sequence identity as compared to a reference sequenceover a comparison region.

Chimeric and Fusion Proteins

The invention also provides protease chimeric or fusion proteins. Asused herein, a protease “chimeric protein” or “fusion protein” comprisesa protease polypeptide operatively-linked to a non-protease polypeptide.A “protease polypeptide” refers to a polypeptide having an amino acidsequence corresponding to one of the scaffolds such as MT-SP1 describedherein or one of the mutants of the MT-SP1 scaffold, whereas a“non-protease polypeptide” refers to a polypeptide having an amino acidsequence corresponding to a protein that is not substantially homologousto one of the scaffolds, e.g., a protein that is different from thescaffold and that is derived from the same or a different organism.Within a protease fusion protein, the protease polypeptide cancorrespond to all or a portion of a parent or scaffold protease protein.In one embodiment, a protease fusion protein comprises at least onebiologically-active portion of a protease protein. In anotherembodiment, a protease fusion protein comprises at least twobiologically-active portions of a protease protein. In yet anotherembodiment, a protease fusion protein comprises at least threebiologically-active portions of a protease protein. Within the fusionprotein, the term “operatively-linked” is intended to indicate that theprotease polypeptide and the non-protease polypeptide are fused in-framewith one another. The non-protease polypeptide can be fused to theN-terminus or C-terminus of the protease polypeptide.

In one embodiment, the fusion protein is a GST-protease fusion proteinin which the protease sequences are fused to the N-terminus of the GST(glutathione S-transferase) sequences. Such fusion proteins canfacilitate the purification of recombinant protease polypeptides.

In another embodiment, the fusion protein is an Fc fusion in which theprotease sequences are fused to the N-terminus of the Fc domain fromimmunoglobulin G. Such fusion proteins can have better pharmacodynamicproperties in vivo.

In another embodiment, the fusion protein is a protease proteincontaining a heterologous signal sequence at its N-terminus. In certainhost cells (e.g., mammalian host cells), expression and/or secretion ofprotease can be increased through use of a heterologous signal sequence.

A protease chimeric or fusion protein of the invention can be producedby standard recombinant DNA techniques. For example, DNA fragmentscoding for the different polypeptide sequences are ligated togetherin-frame in accordance with conventional techniques, e.g., by employingblunt-ended or stagger-ended termini for ligation, restriction enzymedigestion to provide for appropriate termini, filling-in of cohesiveends as appropriate, alkaline phosphatase treatment to avoid undesirablejoining, and enzymatic ligation. In another embodiment, the fusion genecan be synthesized by conventional techniques including automated DNAsynthesizers. Alternatively, PCR amplification of gene fragments can becarried out using anchor primers that give rise to complementaryoverhangs between two consecutive gene fragments that can subsequentlybe annealed and reamplified to generate a chimeric gene sequence (see,e.g., Ausubel et al. (eds.) CURRENT PROTOCOLS IN MOLECULAR BIOLOGY, JohnWiley & Sons, 1992). Moreover, many expression vectors are commerciallyavailable that already encode a fusion moiety (e.g., a GST polypeptide).A protease-encoding nucleic acid can be cloned into such an expressionvector such that the fusion moiety is linked in-frame to the proteaseprotein.

Protease Agonists and Antagonists

The invention also pertains to variants of the protease proteins thatfunction as either protease agonists (i.e., mimetics) or as proteaseantagonists. Variants of the protease protein can be generated bymutagenesis (e.g., discrete point mutation or truncation of the proteaseprotein). An agonist of the protease protein retains substantially thesame, or a subset of, the biological activities of the naturallyoccurring form of the protease protein. For example, an agonist proteaseactivates a target protein (e.g., a cell surface receptor) by cleaving asubstrate sequence within the protein. An antagonist of the proteaseprotein can inhibit one or more of the activities of the naturallyoccurring form of the protease protein by, for example, cleaving thesame target protein as the protease protein. Thus, specific biologicaleffects can be elicited by treatment with a variant of limited function.In one embodiment, treatment of a subject with a variant having a subsetof the biological activities of the naturally occurring form of theprotein has fewer side effects in a subject relative to treatment withthe naturally occurring form of the protease proteins.

Protease Therapy in Combination with Anti-Cancer Agents

Signaling by vascular endothelial growth factor (VEGF) and its receptorsis implicated in pathological angiogenesis and the rapid development oftumor vasculature in cancer. Drugs that block this signaling pathwayprevent the growth and maintenance of tumor blood supply, and lead tothe systematic death of the tumor. The recent success of the anti-VEGFantibody AVASTIN™ in patients with metastatic colon cancer has validatedVEGF as a target for anti-angiogenic therapy of cancer. Despite theseencouraging results, tumor progression has still occurred despiteanti-VEGF treatment. The mechanisms of antibody affecting VEGF functionand how the antibody impedes tumor growth are unknown. Knock downexperiments show that blocking VEGF function blocks angiogenesis. Thusthe inhibition of angiogenic signaling through VEGFR-2 represents anunderdeveloped therapeutic area ideal for the development of engineeredproteases with novel targeting.

Due to their catalytic nature and smaller size, engineered proteasespromise a new therapeutic treatment with advantages over competingtargeted binding proteins. The expected advantages include, but are notlimited to: better tumor penetration, better target saturation, highereffectiveness, and potentially lower dosing. Notably, because they bind,hydrolyze, and release, a single protease could cleave and inactivatehundreds to thousands of substrate VEGF receptors, offering substantialtherapeutic amplification.

In one embodiment, treatment of a pathology, such as a cancer, isprovided comprising administering to a subject in need thereoftherapeutically effective amounts of a protease that specificallycleaves and inactivates the signaling of the VEGF/VEGFR-2 complex, suchas protease MT-SP1 or an MT-SP1 mutein described herein, which isadministered alone or in combination with at least one anti-canceragent. Anti-angiogenic therapy has proven successful against both solidcancers and hematological malignancies. See, e.g., Ribatti et al. 2003 JHematother Stem Cell Res. 12 (1), 11-22. Therefore, compositions of theinvention provided as anti-angiogenic therapy will facilitate thetreatment of both hematological and sold tissue malignancies.Compositions and methods of treatment provided in the invention may beadministered alone or in combination with any other appropriateanti-cancer treatment known to one skilled in the art. For example, theMT-SP1 and MT-SP1 muteins of the invention can be administered incombination with or in place of AVASTIN™ in any therapy where AVASTIN™administration provides therapeutic benefit.

In one embodiment, the anti-cancer agent is at least onechemotherapeutic agent. In a related embodiment, the administering ofthe protease is in combination with at least one radiotherapy.Administration of the combination therapy will attenuate the angiogenicsignal and create a pool of soluble receptor that lowers free VEGFlevels. In a specific embodiment, a variant MT-SP1 protease of theinvention has an in vitro specificity that matches a critical region ofthe receptor, the Flk-1/KDR stalk, over a six amino acid region.

The MT-SP1 mutein polypeptide of the invention may be administered in acomposition containing more than one therapeutic agent. The therapeuticagents may be, for example, therapeutic radionuclides, drugs, hormones,hormone antagonists, receptor antagonists, enzymes or proenzymesactivated by another agent, autocrines, cytokines or any suitableanti-cancer agent known to those skilled in the art. In one embodiment,the anti-cancer agent co-administered with the MT-SP1 or MT-SP1 muteinis AVASTIN™. Toxins also can be used in the methods of the presentinvention. Other therapeutic agents useful in the present inventioninclude anti-DNA, anti-RNA, radiolabeled oligonucleotides, such asantisense oligonucleotides, anti-protein and anti-chromatin cytotoxic orantimicrobial agents. Other therapeutic agents are known to thoseskilled in the art, and the use of such other therapeutic agents inaccordance with the present invention is specifically contemplated.

The antitumor agent may be one of numerous chemotherapy agents such asan alkylating agent, an antimetabolite, a hormonal agent, an antibiotic,an antibody, an anti-cancer biological, Gleevec, colchicine, a vincaalkaloid, L-asparaginase, procarbazine, hydroxyurea, mitotane,nitrosoureas or an imidazole carboxamide. Suitable agents are thoseagents that promote depolarization of tubulin or prohibit tumor cellproliferation. Chemotherapeutic agents contemplated as within the scopeof the invention include, but are not limited to, anti-cancer agentslisted in the Orange Book of Approved Drug Products With TherapeuticEquivalence Evaluations, as compiled by the Food and Drug Administrationand the U.S. Department of Health and Human Services. In addition to theabove chemotherapy agents, the MT-SP1 proteases of the invention mayalso be administered together with radiation therapy treatment.Additional treatments known in the art are contemplated as being withinthe scope of the invention.

The therapeutic agent may be a chemotherapeutic agent. Chemotherapeuticagents are known in the art and include at least the taxanes, nitrogenmustards, ethylenimine derivatives, alkyl sulfonates, nitrosoureas,triazenes, folic acid analogs, pyrimidine analogs, purine analogs, vincaalkaloids, antibiotics, enzymes, platinum coordination complexes,substituted urea, methyl hydrazine derivatives, adrenocorticalsuppressants, or antagonists. More specifically, the chemotherapeuticagents may be one or more agents chosen from the non-limiting group ofsteroids, progestins, estrogens, antiestrogens, or androgens. Even morespecifically, the chemotherapy agents may be azaribine, bleomycin,bryostatin-1, busulfan, carmustine, chlorambucil, cisplatin, CPT-11,cyclophosphamide, cytarabine, dacarbazine, dactinomycin, daunorubicin,dexamethasone, diethylstilbestrol, doxorubicin, ethinyl estradiol,etoposide, fluorouracil, fluoxymesterone, gemcitabine,hydroxyprogesterone caproate, hydroxyurea, L-asparaginase, leucovorin,lomustine, mechlorethamine, medroprogesterone acetate, megestrolacetate, melphalan, mercaptopurine, methotrexate, mithramycin,mitomycin, mitotane, phenyl butyrate, prednisone, procarbazine,semustine streptozocin, tamoxifen, taxanes, taxol, testosteronepropionate, thalidomide, thioguanine, thiotepa, uracil mustard,vinblastine, or vincristine. The use of any combinations of chemotherapyagents is also contemplated. The administration of the chemotherapeuticagent may be before, during or after the administration of the MT-SP1 orthe MT-SP1 mutein polypeptide.

Other suitable therapeutic agents for use in combination or forco-administration with the proteases of the invention are selected fromthe group consisting of radioisotope, boron addend, immunomodulator,toxin, photoactive agent or dye, cancer chemotherapeutic drug, antiviraldrug, antifungal drug, antibacterial drug, antiprotozoal drug andchemosensitizing agent (See, U.S. Pat. Nos. 4,925,648 and 4,932,412).Suitable chemotherapeutic agents are described, for example, inREMINGTON'S PHARMACEUTICAL SCIENCES, 19th Ed. (Mack Publishing Co.1995), and in Goodman and Gilman's THE PHARMACOLOGICAL BASIS OFTHERAPEUTICS (Goodman et al., Eds. Macmillan Publishing Co., New York,1980 and 2001 editions). Other suitable chemotherapeutic agents, such asexperimental drugs, are known to those of skill in the art. Moreover asuitable therapeutic radioisotope is selected from the group consistingof α-emitters, β-emitters, γ-emitters, Auger electron emitters, neutroncapturing agents that emit α-particles and radioisotopes that decay byelectron capture. Preferably, the radioisotope is selected from thegroup consisting of ²²⁵Ac, ¹⁹⁸Au, ³²P, ¹²⁵I, ¹³¹I, ⁹⁰Y, ¹⁸⁶Re, ¹⁸⁸Re,⁶⁷Cu, ¹⁷⁷Lu, ²¹³Bi, ¹⁰B, and ²¹¹At.

Where more than one therapeutic agent is used in combination with theproteases of the invention, they may be of the same class or type or maybe from different classes or types. For example, the therapeutic agentsmay comprise different radionuclides, or a drug and a radionuclide.

In another embodiment, different isotopes that are effective overdifferent distances as a result of their individual energy emissions areused as first and second therapeutic agents in combination with theproteases of the invention. Such agents can be used to achieve moreeffective treatment of tumors, and are useful in patients presentingwith multiple tumors of differing sizes, as in normal clinicalcircumstances.

Few of the available isotopes are useful for treating the very smallesttumor deposits and single cells. In these situations, a drug or toxinmay be a more useful therapeutic agent for co-administration with aprotease of the invention. Accordingly, in some embodiments of thepresent invention, isotopes are used in combination with non-isotopicspecies such as drugs, toxins, and neutron capture agents andco-administered with a protease of the invention. Many drugs and toxinsare known which have cytotoxic effects on cells, and can be used incombination with the proteases of the present invention. They are to befound in compendia of drugs and toxins, such as the Merck Index, Goodmanand Gilman, and the like, and in the references cited above.

Drugs that interfere with intracellular protein synthesis can also beused in combination with a protease in the therapeutic methods of thepresent invention; such drugs are known to those skilled in the art andinclude puromycin, cycloheximide, and ribonuclease.

The therapeutic methods of the invention may be used for cancer therapy.It is well known that radioisotopes, drugs, and toxins can be conjugatedto antibodies or antibody fragments which specifically bind to markerswhich are produced by or associated with cancer cells, and that suchantibody conjugates can be used to target the radioisotopes, drugs ortoxins to tumor sites to enhance their therapeutic efficacy and minimizeside effects. Examples of these agents and methods are reviewed inWawrzynczak and Thorpe (in Introduction to the Cellular and MolecularBiology of Cancer, L. M. Franks and N. M. Teich, eds, Chapter 18, pp.378-410, Oxford University Press. Oxford, 1986), in Immunoconjugates:Antibody Conjugates in Radioimaging and Therapy of Cancer (C. W. Vogel,ed., 3-300, Oxford University Press, N.Y., 1987), in Dillman, R. O. (CRCCritical Reviews in Oncology/Hematology 1:357, CRC Press, Inc., 1984),in Pastan et al. (Cell 47:641, 1986), in Vitetta et al. (Science238:1098-1104, 1987), and in Brady et al. (Int. J. Rad. Oncol. Biol.Phys. 13:1535-1544, 1987). Other examples of the use of immunoconjugatesfor cancer and other forms of therapy have been disclosed, inter alia,in U.S. Pat. Nos. 4,331,647, 4,348,376, 4,361,544, 4,468,457, 4,444,744,4,460,459, 4,460,561 4,624,846, 4,818,709, 4,046,722, 4,671,958,4,046,784, 5,332,567, 5,443,953, 5,541,297, 5,601,825, 5,635,603,5,637,288, 5,677,427, 5,686,578, 5,698,178, 5,789,554, 5,922,302,6,187,287, and 6,319,500.

Additionally, the treatment methods of the invention include those inwhich a protease of the invention is used in combination with othercompounds or techniques for preventing, mitigating or reversing the sideeffects of certain cytotoxic agents. Examples of such combinationsinclude, e.g., administration of IL-1 together with an antibody forrapid clearance, as described in e.g., U.S. Pat. No. 4,624,846. Suchadministration can be performed from 3 to 72 hours after administrationof a primary therapeutic treatment with a MT-SP1 mutein in combinationwith a anti-cancer agent (e.g., with a radioisotope, drug or toxin asthe cytotoxic component). This can be used to enhance clearance of theconjugate, drug or toxin from the circulation and to mitigate or reversemyeloid and other hematopoietic toxicity caused by the therapeuticagent.

In another aspect of the invention, and as noted above, cancer therapymay involve a combination of more than one tumoricidal agent, e.g., adrug and a radioisotope, or a radioisotope and a Boron-10 agent forneutron-activated therapy, or a drug and a biological response modifier,or a fusion molecule conjugate and a biological response modifier. Thecytokine can be integrated into such a therapeutic regimen to maximizethe efficacy of each component thereof.

Similarly, certain antileukemic and antilymphoma antibodies conjugatedwith radioisotopes that are β or α emitters may induce myeloid and otherhematopoietic side effects when these agents are not solely directed tothe tumor cells. This is observed particularly when the tumor cells arein the circulation and in the blood-forming organs. Concomitant and/orsubsequent administration of at least one hematopoietic cytokine (e.g.,growth factors, such as colony stimulating factors, such as G-CSF andGM-CSF) is preferred to reduce or ameliorate the hematopoietic sideeffects, while augmenting the anticancer effects.

It is well known in the art that various methods of radionuclide therapycan be used for the treatment of cancer and other pathologicalconditions, as described, e.g., in Harbert, “Nuclear Medicine Therapy”,New York, Thieme Medical Publishers, 1087, pp. 1-340. A clinicianexperienced in these procedures will readily be able to adapt thecytokine adjuvant therapy described herein to such procedures tomitigate any hematopoietic side effects thereof. Similarly, therapy withcytotoxic drugs, co-administered with MT-SP1 or a MT-SP1 mutein, can beused, e.g., for treatment of cancer, infectious or autoimmune diseases,and for organ rejection therapy. Such treatment is governed by analogousprinciples to radioisotope therapy with isotopes or radiolabeledantibodies. Thus, the ordinary skilled clinician will be able to adaptthe description of cytokine use to mitigate marrow suppression and othersuch hematopoietic side effects by administration of the cytokinebefore, during and/or after the primary anti-cancer therapy.

Pharmaceutical Compositions

Sequential or substantially simultaneous administration of eachtherapeutic MT-SP1 and other therapeutic agents combined with theprotease can be effected by any appropriate route including, but notlimited to, oral routes, intravenous routes, intramuscular routes, anddirect absorption through mucous membrane tissues. MT-SP1 and othertherapeutic agents can be administered by the same route or by differentroutes. For example, MT-SP1 may be administered by intravenous injectionwhile the other therapeutic agent(s) of the combination may beadministered orally. Alternatively, for example, the other therapeuticagent(s) may be administered by intravenous injection. The sequence inwhich the therapeutic agents are administered is not narrowly critical.

Administration of MT-SP1 also can be accompanied by the administrationof the other therapeutic agents as described above in furthercombination with other biologically active ingredients and non-drugtherapies (e.g., surgery or radiation treatment) or with non-drugtherapies alone with MT-SP1. Where the combination therapy furthercomprises a non-drug treatment, the non-drug treatment may be conductedat any suitable time so long as a beneficial effect from the co-actionof the combination of the therapeutic agents and non-drug treatment isachieved. For example, in appropriate cases, the beneficial effect isstill achieved when the non-drug treatment is temporally removed fromthe administration of the therapeutic agents, perhaps by days or evenweeks.

Thus, MT-SP1 and the other pharmacologically active agent may beadministered to a patient simultaneously, sequentially or incombination. If administered sequentially, the time betweenadministrations generally varies from 0.1 to about 48 hours. It will beappreciated that when using MT-SP1 with other therapeutic agent(s), theymay be in the same pharmaceutically acceptable carrier and thereforeadministered simultaneously. They may be in separate pharmaceuticalcarriers such as conventional oral dosage forms which are takensimultaneously.

A therapy for a angiogenic condition includes MT-SP1 and AVASTIN™. Inone embodiment, this condition is cancer.

A therapy for cancer, inflammation, diabetes or macular degenerationincludes MT-SP1. In another embodiment, this therapy further includesanother therapeutic as defined above.

Advantages attributed to the administration of MT-SP1 and at least asecond agent as part of a specific treatment regimen includes, but isnot limited to, pharmacokinetic or pharmacodynamic co-action resultingfrom the combination of therapeutic agents. In one embodiment, theco-action of the therapeutic agents is additive. In another embodiment,the co-action of the therapeutic agents is synergistic. In anotherembodiment, the co-action of the therapeutic agents improves thetherapeutic regimen of one or both of the agents.

The invention further relates to kits for treating patients having anangiogenic condition, such as cancer, comprising a therapeuticallyeffective dose of MT-SP1 for treating or at least partially alleviatingthe symptoms of the condition (e.g., AVASTIN™), either in the same orseparate packaging, and instructions for its use.

The present invention is suitable for the reduction of cancer symptoms.These cancer symptoms include blood in the urine, pain or burning uponurination, frequent urination, cloudy urine, pain in the bone orswelling around the affected site, fractures in bones, weakness,fatigue, weight loss, repeated infections, nausea, vomiting,constipation, problems with urination, weakness or numbness in the legs,bumps and bruises that persist, dizziness, drowsiness, abnormal eyemovements or changes in vision, weakness, loss of feeling in arms orlegs or difficulties in walking, fits or convulsions, changes inpersonality, memory or speech, headaches that tend to be worse in themorning and ease during the day, that may be accompanied by nausea orvomiting, a lump or thickening of the breast, discharge from the nipple,change in the skin of the breast, a feeling of heat, or enlarged lymphnodes under the arm, rectal bleeding (red blood in stools or blackstools), abdominal cramps, constipation alternating with diarrhea,weight loss, loss of appetite, weakness, pallid complexion, dull ache orpain in the back or side, lump in kidney area, sometimes accompanied byhigh blood pressure or abnormality in red blood cell count, weakness,paleness, fever and flu-like symptoms, bruising and prolonged bleeding,enlarged lymph nodes, spleen, liver, pain in bones and joints, frequentinfections, weight loss, night sweats, wheezing, persistent cough formonths, blood-streaked sputum, persistent ache in chest, congestion inlungs, enlarged lymph nodes in the neck, change in mole or other bump onthe skin, including bleeding or change in size, shape, color, ortexture, painless swelling in the lymph nodes in the neck, underarm, orgroin, persistent fever, feeling of fatigue, unexplained weight loss,itchy skin and rashes, small lumps in skin, bone pain, swelling in theabdomen, liver or spleen enlargement, a lump in the mouth, ulceration ofthe lip, tongue or inside of the mouth that does not heal within acouple of weeks, dentures that no longer fit well, oral pain, bleeding,foul breath, loose teeth, changes in speech, abdominal swelling,abnormal vaginal bleeding, digestive discomfort, upper abdominal pain,unexplained weight loss, pain near the center of the back, intoleranceof fatty foods, yellowing of the skin, abdominal masses, enlargement ofliver and spleen, urination difficulties due to blockage of the urethra,bladder retains urine, creating frequent feelings of urgency to urinate,especially at night, bladder not emptying completely, burning or painfulurination, bloody urine, tenderness over the bladder, dull ache in thepelvis or back, indigestion or heartburn, discomfort or pain in theabdomen, nausea and vomiting, diarrhea or constipation, bloating aftermeals, loss of appetite, weakness and fatigue, bleeding—vomiting bloodor blood in the stool, abnormal vaginal bleeding, a watery bloodydischarge in postmenopausal women, a painful urination, pain duringintercourse, and pain in pelvic area

Preferably, treatment should continue as long as cancer symptoms aresuspected or observed.

The present invention is suitable for the reduction of maculardegeneration symptoms. These macular degeneration symptoms includeblurring of vision, lines forming in vision and gradual or quick loss ofvision.

The present invention is suitable for the reduction of diabetessymptoms. These diabetes symptoms include loss of vision and blindness.

To evaluate whether a patient is benefiting from the (treatment), onewould examine the patient's symptoms in a quantitative way, by decreasein the frequency of relapses, or increase in the time to sustainedprogression, or improvement and compare the patient's status measurementbefore and after treatment. In a successful treatment, the patientstatus will have improved. Measurement number or frequency of relapseswill have decreased, or the time to sustained progression will haveincreased.

As for every drug, the dosage is an important part of the success of thetreatment and the health of the patient. In every case, in the specifiedrange, the physician has to determine the best dosage for a givenpatient, according to gender, age, weight, height, pathological stateand other parameters.

The pharmaceutical compositions of the present invention contain atherapeutically effective amount MT-SP1. The amount of the compound willdepend on the patient being treated. The patient's weight, severity ofillness, manner of administration and judgment of the prescribingphysician should be taken into account in deciding the proper amount.The determination of a therapeutically effective amount of MT-SP1 orother therapeutic agent is well within the capabilities of one withskill in the art.

In some cases, it may be necessary to use dosages outside of the rangesstated in pharmaceutical packaging insert to treat a patient. Thosecases will be apparent to the prescribing physician. Where it isnecessary, a physician will also know how and when to interrupt, adjustor terminate treatment in conjunction with a response of a particularpatient.

Formulation (Separately or Together) and Administration

The compounds of the present invention are administered separately orco-formulated in a suitable co-formulated dosage form. Compounds,including those used in combination therapies are administered to apatient in the form of a pharmaceutically acceptable salt or in apharmaceutical composition. A compound that is administered in apharmaceutical composition is mixed with a suitable carrier or excipientsuch that a therapeutically effective amount is present in thecomposition. The term “therapeutically effective amount” refers to anamount of the compound that is necessary to achieve a desired endpoint(e.g., decreasing symptoms associated with cancer).

A variety of preparations can be used to formulate pharmaceuticalcompositions containing MT-SP1 and other therapeutic agents. Techniquesfor formulation and administration may be found in “Remington: TheScience and Practice of Pharmacy, Twentieth Edition,” LippincottWilliams & Wilkins, Philadelphia, Pa. Tablets, capsules, pills, powders,granules, dragees, gels, slurries, ointments, solutions suppositories,injections, inhalants and aerosols are examples of such formulations.The formulations can be administered in either a local or systemicmanner or in a depot or sustained release fashion. Administration of thecomposition can be performed in a variety of ways. The compositions andcombination therapies of the invention may be administered incombination with a variety of pharmaceutical excipients, includingstabilizing agents, carriers and/or encapsulation formulations asdescribed herein.

The preparation of pharmaceutical or pharmacological compositions willbe known to those of skill in the art in light of the presentdisclosure. Typically, such compositions may be prepared as injectables,either as liquid solutions or suspensions; solid forms suitable forsolution in, or suspension in, liquid prior to injection; as tablets orother solids for oral administration; as time release capsules; or inany other form currently used, including creams, lotions, mouthwashes,inhalants and the like.

For human administration, preparations should meet sterility,pyrogenicity, general safety and purity standards as required by theFDA.

Administration of compounds alone or in combination therapies may be,e.g., subcutaneous, intramuscular or intravenous injection, or any othersuitable route of administration. A particularly convenient frequencyfor the administration of the compounds of the invention is once a day.

Upon formulation, therapeutics will be administered in a mannercompatible with the dosage formulation, and in such amount as ispharmacologically effective. The formulations are easily administered ina variety of dosage forms, such as the injectable solutions described,but drug release capsules and the like can also be employed. In thiscontext, the quantity of active ingredient and volume of composition tobe administered depends on the host animal to be treated. Preciseamounts of active compound required for administration depend on thejudgment of the practitioner and are peculiar to each individual.

A minimal volume of a composition required to disperse the activecompounds is typically utilized. Suitable regimes for administration arealso variable, but would be typified by initially administering thecompound and monitoring the results and then giving further controlleddoses at further intervals.

A carrier can be a solvent or dispersion medium containing, for example,water, ethanol, polyol (for example, glycerol, propylene glycol, andliquid polyethylene glycol, and the like), suitable mixtures thereof,and vegetable oils. The proper fluidity can be maintained, for example,by the use of a coating, such as lecithin, by the maintenance of therequired particle size in the case of dispersion and by the use ofsurfactants. The prevention of the action of microorganisms can bebrought about by various antibacterial and antifungal agents, forexample, parabens, chlorobutanol, phenol, sorbic acid, thimerosal, andthe like. In many cases, it will be preferable to include isotonicagents, for example, sugars or sodium chloride. Prolonged absorption ofthe injectable compositions can be brought about by the use in thecompositions of agents delaying absorption, for example, aluminummonostearate and gelatin.

Suitable preservatives for use in solution include benzalkoniumchloride, benzethonium chloride, chlorobutanol, thimerosal and the like.Suitable buffers include boric acid, sodium and potassium bicarbonate,sodium and potassium borates, sodium and potassium carbonate, sodiumacetate, sodium biphosphate and the like, in amounts sufficient tomaintain the pH at between about pH 6 and pH 8, and preferably, betweenabout pH 7 and pH 7.5. Suitable tonicity agents are dextran 40, dextran70, dextrose, glycerin, potassium chloride, propylene glycol, sodiumchloride, and the like, such that the sodium chloride equivalent of theophthalmic solution is in the range 0.9 plus or minus 0.2%. Suitableantioxidants and stabilizers include sodium bisulfite, sodiummetabisulfite, sodium thiosulfite, thiourea and the like. Suitablewetting and clarifying agents include polysorbate 80, polysorbate 20,poloxamer 282 and tyloxapol. Suitable viscosity-increasing agentsinclude dextran 40, dextran 70, gelatin, glycerin,hydroxyethylcellulose, hydroxmethylpropylcellulose, lanolin,methylcellulose, petrolatum, polyethylene glycol, polyvinyl alcohol,polyvinylpyrrolidone, carboxymethylcellulose and the like.

The compounds and combination therapies of the invention can beformulated by dissolving, suspending or emulsifying in an aqueous ornonaqueous solvent. Vegetable (e.g., sesame oil, peanut oil) or similaroils, synthetic aliphatic acid glycerides, esters of higher aliphaticacids and propylene glycol are examples of nonaqueous solvents. Aqueoussolutions such as Hank's solution, Ringer's solution or physiologicalsaline buffer can also be used. In all cases the form must be sterileand must be fluid to the extent that easy syringability exists. It mustbe stable under the conditions of manufacture and storage and must bepreserved against the contaminating action of microorganisms, such asbacteria and fungi.

Solutions of active compounds as free base or pharmacologicallyacceptable salts can be prepared in water suitably mixed with asurfactant, such as hydroxypropylcellulose. Dispersions can also beprepared in glycerol, liquid polyethylene glycols, and mixtures thereofand in oils. Under ordinary conditions of storage and use, thesepreparations contain a preservative to prevent the growth ofmicroorganisms.

Sterile injectable solutions are prepared by incorporating the activecompounds in the required amount in the appropriate solvent with variousof the other ingredients enumerated above, as required, followed byfiltered sterilization. Generally, dispersions are prepared byincorporating the various sterilized active ingredients into a sterilevehicle which contains the basic dispersion medium and the requiredother ingredients from those enumerated above. In the case of sterilepowders for the preparation of sterile injectable solutions, thepreferred methods of preparation are vacuum-drying and freeze-dryingtechniques which yield a powder of the active ingredient plus anyadditional desired ingredient from a previously sterile-filteredsolution thereof.

The preparation of more, or highly, concentrated solutions forsubcutaneous or intramuscular injection is also contemplated. In thisregard, the use of DMSO as solvent is preferred as this will result inextremely rapid penetration, delivering high concentrations of theactive compound(s) or agent(s) to a small area.

Where one or both active ingredients of the combination therapy is givenorally, it can be formulated through combination with pharmaceuticallyacceptable carriers that are well known in the art. The carriers enablethe compound to be formulated, for example, as a tablet, pill, capsule,solution, suspension, sustained release formulation; powder, liquid orgel for oral ingestion by the patient. Oral use formulations can beobtained in a variety of ways, including mixing the compound with asolid excipient, optionally grinding the resulting mixture, addingsuitable auxiliaries and processing the granule mixture. The followinglist includes examples of excipients that can be used in an oralformulation: sugars such as lactose, sucrose, mannitol or sorbitol;cellulose preparations such as maize starch, wheat starch, potatostarch, gelatin, gum tragacanth, methyl cellulose,hydroxypropylmethylcellulose, sodium carboxymethylcellulose andpolyvinylpyrrolidone (PVP). Oral formulations include such normallyemployed excipients as, for example, pharmaceutical grades of mannitol,lactose, starch, magnesium stearate, sodium saccharine, cellulose,magnesium carbonate and the like.

In certain defined embodiments, oral pharmaceutical compositions willcomprise an inert diluent or assimilable edible carrier, or they may beenclosed in hard or soft shell gelatin capsule, or they may becompressed into tablets, or they may be incorporated directly with thefood of the diet. For oral therapeutic administration, the activecompounds may be incorporated with excipients and used in the form ofingestible tablets, buccal tables, troches, capsules, elixirs,suspensions, syrups, wafers, and the like. Such compositions andpreparations should contain at least 0.1% of active compound. Thepercentage of the compositions and preparations may, of course, bevaried and may conveniently be between about 2 to about 75% of theweight of the unit, or preferably between 25-60%. The amount of activecompounds in such therapeutically useful compositions is such that asuitable dosage will be obtained.

The tablets, troches, pills, capsules and the like may also contain thefollowing: a binder, as gum tragacanth, acacia, cornstarch, or gelatin;excipients, such as dicalcium phosphate; a disintegrating agent, such ascorn starch, potato starch, alginic acid and the like; a lubricant, suchas magnesium stearate; and a sweetening agent, such as sucrose, lactoseor saccharin may be added or a flavoring agent, such as peppermint, oilof wintergreen, or cherry flavoring. When the dosage unit form is acapsule, it may contain, in addition to materials of the above type, aliquid carrier. Various other materials may be present as coatings or tootherwise modify the physical form of the dosage unit. For instance,tablets, pills, or capsules may be coated with shellac, sugar or both. Asyrup of elixir may contain the active compounds sucrose as a sweeteningagent methyl and propylparabensas preservatives, a dye and flavoring,such as cherry or orange flavor.

Additional formulations suitable for other modes of administrationinclude suppositories. For suppositories, traditional binders andcarriers may include, for example, polyalkylene glycols ortriglycerides; such suppositories may be formed from mixtures containingthe active ingredient in the range of 0.5% to 10%, preferably 1%-2%.

The subject treated by the methods of the invention is a mammal, morepreferably a human. The following properties or applications of thesemethods will essentially be described for humans although they may alsobe applied to non-human mammals, e.g., apes, monkeys, dogs, mice, etc.The invention therefore can also be used in a veterinarian context.

The following examples are nonlimiting and meant only to illustratevarious aspects of the invention.

EXAMPLES Example 1 Methods of Cloning and Characterizing EngineeredMT-SP1 Protease with Altered Substrate Specificity Based on WellUnderstood Starting Scaffolds

The serine protease MT-SP1 has been chosen as scaffold protease formutagenesis towards specific proteolysis of VEGF and VEGFR in partbecause it has been well characterized with biochemical and structuraltechniques [Harris, Recent Results Cancer Res. 1998; 152:341-52].

MT-SP1 is a membrane bound serine protease with multiple extracellularprotein-protein interaction domains. The protease domain alone has beenprofiled using the totally diverse and P1-Lys PSSCL (FIG. 4A-4C)revealing an extended specificity of (basic)-(non-basic)-Ser-Arg or(non-basic)-(basic)-Ser-Arg/Lys. The X-ray crystallographic structure ofMT-SP1 reveals components proposed to regulate activity and a nine aminoacid insertion in the 60's loop that may determine P2 specificity

Variants of MT-SP1 have been created and characterized. Various proteasemuteins have been expressed and purified, as described below. Initialactivity to verify activity and specificity have been performed, andsample results are provided in FIGS. 1-11.

Example 2 Expression and Purification of MT-SP1

A mutated MT-SP1 polypeptide (“mutein”) may contain a single mutationper polypeptide, or may contain two or more mutated residues in anycombination, as illustrated in Table 11.

Wild-type and mutant MT-SP1 are cloned into the pQE bacterial expressionvector (Qiagen) containing an N-terminal 6 histidine tag, prodomain, andprotease domain and the resulting constructs transformed into BL21 E.coli cells. Cells are grown in 100 mL cultures to an OD of 0.6, andexpression of the protease in inclusion bodies is induced by adding IPTGto a final concentration of 1 mM. After 4-6 hours, the bacteria arepelleted by centrifugation and the pellet resuspended in 50 mM Tris pH8, 500 mM KCl, and 10% glycerol (buffer A). Cells are lysed bysonication and pelleted by centrifugation at 6000×g. Pellets areresuspended in 50 mM Tris pH 8, 6 M urea, 100 mM NaCl and 1%2-mercaptoethanol (buffer B). Membrane and organelles are pelleted bycentrifugation at 10,000×g and the supernatant is passed over a nickelNTA column (Qiagen). The column is washed with 50 mM Tris pH8, 6 M urea,100 mM NaCl, 20 mM imidazole, 1% 2-mercaptoethanoland 0.01% Tween 20(buffer D). The column is washed again with buffer D without Tween 20.The protease is then eluted from the column with 50 mM Tris pH 8, 6 Murea, 100 mM NaCl, 1% 2-mercaptoethanol and 250 mM imidazole (buffer E).The protease is then concentrated to a volume of ˜1 mL and then dialyzedat 4° C. overnight in 1 L of 50 mM Tris pH8, 3 M urea, 100 mM NaCl, 1%2-mercaptoethanol, and 10% glycerol. Finally, the protease is dialyzedinto 50 mM Tris pH 8, 100 mM NaCl, and 10% glycerol at 4° C. overnight.During the last dialysis step; the protease becomes autoactivated byself-cleavage, resulting in the removal of the 6 histidine tag andprodomain.

Result. Multi-milligram quantities are obtained using this bacterialexpression system. The protease is produced in inclusion bodies and ispurified by a one-column purification procedure and then re-foldedthrough successive dialysis steps (FIG. 1). Once refolded, the proteaseactivates itself by cleavage at the juncture between the prodomain andthe protease domain at the sequence RQAR (SEQ ID NO: 18)/VVGG (SEQ IDNO:6).

Example 3 Synthesis and Screening of Combinatorial Libraries forCharacterization of MT-SP1 Wild-Type and Muteins

Fixed P1 Amino Acid Method

Individual P1-substituted Fmoc-amino acid ACC-resin (ca. 25 mg, 0.013mmol) was added to wells of a Multi-Chem 96-well reaction apparatus. Theresin-containing wells were solvated with DMF (0.5 mL). A 20% piperidinein DMF solution (0.5 mL) was added followed by agitation for 30 min. Thewells of the reaction block were filtered and washed with DMF (3×0.5mL). In order to introduce the randomized P2 position, an isokineticmixture (Ostresh, J. M., et al., (1994) Biopolymers 34:1681-9) ofFmoc-amino acids (4.8 mmol, 10 equiv/well; Fmoc-amino acid, mol %:Fmoc-Ala-OH, 3.4; Fmoc-Arg(Pbf)-OH, 6.5; Fmoc-Asn(Trt)-OH, 5.3;Fmoc-Asp(O-t-Bu)-OH, 3.5; Fmoc-Glu(O-t-Bu)-OH, 3.6; Fmoc-Gln(Trt)-OH,5.3; Fmoc-Gly-OH, 2.9; Fmoc-His(Trt)-OH, 3.5; Fmoc-Ile-OH, 17.4;Fmoc-Leu-OH, 4.9; Fmoc-Lys(Boc)-OH, 6.2; Fmoc-Nle-OH, 3.8; Fmoc-Phe-OH,2.5; Fmoc-Pro-OH, 4.3; Fmoc-Ser(O-t-Bu)-OH, 2.8; Fmoc-Thr(O-t-Bu)-OH,4.8; Fmoc-Trp(Boc)-OH, 3.8; Fmoc-Tyr(O-t-Bu)-OH, 4.1; Fmoc-Val-OH, 11.3)was pre-activated with DICI (390 μL, 2.5 mmol), and HOBt (340 mg, 2.5mmol) in DMF (10 mL). The solution (0.5 mL) was added to each of thewells. The reaction block was agitated for 3 h, filtered, and washedwith DMF (3×0.5 mL). The randomized P3 and P4 positions wereincorporated in the same manner. The Fmoc of the P4 amino acid wasremoved and the resin was washed with DMF (3×0.5 mL), and treated with0.5 mL of a capping solution of AcOH (150 μL, 2.5 mmol), HOBt (340 mg,2.5 mmol) and DICI (390 μL, 2.5 mmol) in DMF (10 mL). After 4 h ofagitation, the resin was washed with DMF (3×0.5 mL), CH₂Cl₂ (3×0.5 mL),and treated with a solution of 95:2.5:2.5 TFA/TIS/H₂O. After incubatingfor 1 h the reaction block was opened and placed on a 96 deep-well titerplate and the wells were washed with additional cleavage solution (2×0.5mL). The collection plate was concentrated, and the substrate-containingwells were diluted with EtOH (0.5 mL) and concentrated twice. Thecontents of the individual wells were lyophilized from CH₃CN:H₂Omixtures. The total amount of substrate in each well was conservativelyestimated to be 0.0063 mmol (50%) based upon yields of singlesubstrates.

P1-Diverse Amino Acid Method

7-Fmoc-aminocoumarin-4-acetic acid was prepared by treating7-aminocoumarin-4-acetic acid with Fmoc-Cl. 7-Aminocoumarin-4-aceticacid (10.0 g, 45.6 mmol) and H₂O (228 ml) were mixed. NaHCO₃ (3.92 g,45.6 mmol) was added in small portions followed by the addition ofacetone (228 ml). The solution was cooled with an ice bath, and Fmoc-Cl(10.7 g, 41.5 mmol) was added with stirring over the course of 1 h. Theice bath was removed and the solution was stirred overnight. The acetonewas removed with rotary evaporation and the resulting gummy solid wascollected by filtration and washed with several portions of hexane.ACC-resin was prepared by condensation of Rink Amide AM resin with7-Fmoc-aminocoumarin-4-acetic acid. Rink Amide AM resin (21 g, 17 mmol)was solvated with DMF (200 ml). The mixture was agitated for 30 min andfiltered with a filter cannula, whereupon 20% piperidine in DMF (200 ml)was added. After agitation for 25 min, the resin was filtered and washedwith DMF (3 times, 200 ml each). 7-Fmoc-aminocoumarin-4-acetic acid (15g, 34 mmol), HOBt (4.6 g, 34 mmol), and DMF (150 ml) were added,followed by diisopropylcarbodiimide (DICI) (5.3 ml, 34 mmol). Themixture was agitated overnight, filtered, washed (DMF, three times with200 ml; tetrahydrofuran, three times with 200 ml; MeOH, three times with200 ml), and dried over P₂O₅. The substitution level of the resin was0.58 mmol/g (>95%) as determined by Fmoc analysis.

P1-Diverse Library Synthesis

Individual P1-substituted Fmoc-amino acid ACC-resin (˜25 mg, 0.013 mmol)was added to wells of a MultiChem 96-well reaction apparatus. Theresin-containing wells were solvated with DMF (0.5 ml). Afterfiltration, 20% piperidine in DMF solution 30 (0.5 ml) was added,followed by agitation for 30 min. The wells of the reaction block werefiltered and washed with DMF (three times with 0.5 ml). To introduce therandomized P2 position, an isokinetic mixture of Fmoc-amino acids [4.8mmol, 10 eq per well; Fmoc-amino acid, mol %: Fmoc-Ala-OH, 3.4;Fmoc-Arg(Pbf)-OH, 6.5; Fmoc-Asn(Trt)-OH, 5.3; Fmoc-Asp(O-t-Bu)-OH, 3.5;Fmoc-Glu(O-t-Bu)-OH, 3.6; Fmoc-Gln(Trt)-OH, 5.3; Fmoc-Gly-OH, 2.9;Fmoc-His(Trt)-OH, 3.5; Fmoc-Ile-OH, 17.4; Fmoc-Leu-OH, 4.9;Fmoc-Lys(Boc)-OH, 6.2; Fmoc-Nle-OH, 3.8; Fmoc-Phe-OH, 2.5; Fmoc-Pro-OH,4.3; Fmoc-Ser(O-t-Bu)-OH, 2.8; Fmoc-Thr(O-t-Bu)-OH, 4.8;Fmoc-Trp(Boc)-OH, 3.8; Fmoc-Tyr(O-t-Bu)-OH, 4.1; Fmoc-Val-OH, 11.3] waspreactivated with DICI (390 μl, 2.5 mmol), and HOBt (340 mg, 2.5 mmol)in DMF (10 ml). The solution (0.5 ml) was added to each of the wells.The reaction block was agitated for 3 h, filtered, and washed with DMF(three times with 0.5 ml). The randomized P3 and P4 positions wereincorporated in the same manner. The Fmoc of the P4 amino acid wasremoved and the resin was washed with DMF (three times with 0.5 ml) andtreated with 0.5 ml of a capping solution of AcOH (150 μl, 2.5 mmol),HOBt (340 mg, 2.5 mmol), and DICI (390 μl, 2.5 mmol) in DMF (10 ml).After 4 h of agitation, the resin was washed with DMF (three times with0.5 ml) and CH₂Cl₂ (three times with 0.5 ml), and treated with asolution of 95:2.5:2.5 TFA/TIS/H₂O. After incubation for 1 h thereaction block was opened and placed on a 96-deep-well titer plate andthe wells were washed with additional cleavage solution (twice with 0.5ml). The collection plate was concentrated, and the material in thesubstrate-containing wells was diluted with EtOH (0.5 ml) andconcentrated twice. The contents of the individual wells werelyophilized from CH₃CN/H₂O mixtures. The total amount of substrate ineach well was conservatively estimated to be 0.0063 mmol (50%) on thebasis of yields of single substrates.

Screening Methods Using Both Libraries

Multigram quantities of P1-substituted ACC-resin can be synthesized bythe methods described. Fmoc-amino acid-substituted ACC resin was placedin 57 wells of a 96-well reaction block: sub-libraries were denoted bythe second fixed position (P4, P3, P2) of 19 amino acids (cysteine wasomitted and norleucine was substituted for methionine). Synthesis,capping, and cleavage of the substrates were identical to thosedescribed in the previous section, with the exception that for P2, P3,and P4 sub-libraries, individual amino acids (5 eq of Fmoc-amino acidmonomer, 5 eq of DICI, and 5 eq of HOBt in DMF), rather than isokineticmixtures, were incorporated in the spatially addressed P2, P3, or P4positions.

Preparation of the complete diverse and P1-fixed combinatorial librarieswas carried out as described above. The library was aliquoted into96-well plates to a final concentration of 250 μM. Variant proteaseswere diluted in MTSP activity buffer (50 mM Na Hepes, pH 8.0, 100 mMNaCl, 0.01% Tween-20) to concentrations between 50 nM and 1 μM. Initialactivity against Ac-QGR-AMC was used to adjust the variant proteaseconcentration to one approximately equal to 50 nM wild type rat MT-SP1.Enzymatic activity in the P1-Arg library was assayed for one hour at 30°C. on a Spectra-Max Delta flourimeter (Molecular Devices). Excitationand emission were measured at 380 nm and 460 nm, respectively.

Synthesis and Fluorescence Screening of Libraries.

P1-Diverse Library

A(i). Synthesis

P1-diverse libraries were synthesized as provided above. The specificityof the various MT-SP1 muteins were characterized as compared towild-type MT-SP1.

A(ii). Enzymatic Assay of Library

The concentration of proteolytic enzymes was determined by absorbancemeasured at 280 nm (Gill, S. C., et al., (1989) Anal Biochem182:319-26). The proportion of catalytically active thrombin, plasmin,trypsin, uPA, tPA, and chymotrypsin was quantitated by active-sitetitration with MUGB or MUTMAC (Jameson, G. W., et al., (1973)Biochemical Journal 131:107-117).

Substrates from the PSSCLs were dissolved in DMSO. Approximately1.0×10⁻⁹ mol of each P1-Lys, P1-Arg, or P1-Leu sub-library (361compounds) was added to 57 wells of a 96-well microfluor plate (DynexTechnologies, Chantilly, Va.) for a final concentration of 0.1 μM.Approximately 1.0×10⁻¹⁰ mol of each P1-diverse sub-library (6859compounds) was added to 20 wells of a 96-well plate for a finalconcentration of 0.01 μM in each compound. Hydrolysis reactions wereinitiated by the addition of enzyme (0.02 nM-100 nM) and monitoredfluorimetrically with a Perkin Elmer LS50B Luminescence Spectrometer,with excitation at 380 nm and emission at 450 nm or 460 nm. Assays ofthe serine proteases were performed at 25° C. in a buffer containing 50mM Tris, pH 8.0, 100 mM NaCl, 0.5 mM CaCl₂, 0.01% Tween-20, and 1% DMSO(from substrates). Assay of the cysteine proteases, papain and cruzain,was performed at 25° C. in a buffer containing 100 mM sodium acetate, pH5.5, 100 mM NaCl, 5 mM DTT, 1 mM EDTA, 0.01% Brij-35, and 1% DMSO (fromsubstrates).

B. Profiling Proteases with a P1-Diverse Library of 137,180 SubstrateSequences

To test the possibility of attaching all amino acids to the P1-site inthe substrate sequence a P1-diverse tetrapeptide library was created.The P1-diverse library consists of 20 wells in which only theP1-position is systematically held constant as all amino acids,excluding cysteine and including norleucine. The P2, P3, and P4positions consist of an equimolar mixture of all amino acids for a totalof 6,859 substrate sequences per well. Several serine and cysteineproteases were profiled to test the applicability of this library forthe identification of the optimal P1 amino acid. Chymotrypsin showed theexpected specificity for large hydrophobic amino acids. Trypsin andthrombin showed preference for P1-basic amino acids (Arg>Lys). Plasminalso showed a preference for basic amino acids (Lys>Arg). Granzyme B,the only known mammalian serine protease to have P1-Asp specificity,showed a distinct preference for aspartic acid over all other aminoacids, including the other acidic amino acid, Glu. The P1-profile forhuman neutrophil elastase has the canonical preference for alanine andvaline. The cysteine proteases, papain and cruzain showed the broadP1-substrate sequence specificity that is known for these enzymes,although there is a modest preference for arginine. The MT-SP1 wild typeprotease preferred Arg or Lys.

C. Profiling MT-SP1 Proteases with the P1-Constant Library

A P1-constant tetrapeptide library is created as disclosed above. TheP1-constant library consists of 20 wells in which only the P1-positionis systematically held constant as all amino acids, excluding cysteineand including norleucine. The P2, P3, and P4 positions consist of anequimolar mixture of all amino acids for a total of 6,859 substratesequences per well. Several serine and cysteine proteases were profiledto test the applicability of this library for the identification of theoptimal P1 amino acid. MT-SP1 prefers the amino acids Arg and Lys at P1.

Example 4 Determination of the Extended Specificity of MT-SP1 Variantsby PSSCL

The P1-Arg fixed PSSCL library is resuspended in DMSO and arrayed inopaque black 96-well plates at a concentration of 5-10 nanomoles perwell. Variant proteases are diluted into 50 mM Tris pH 8, 50 mM NaCl,and 0.01% Tween 20 (MTSP activation buffer) at a concentration of 5 nMto 5 μM. One hundred microliters of the protease solution is added toeach well and fluorescence of the ACC leaving group is measured byexcitation at 380 nm and emission at 460 nm using a Spectramaxfluorescent plate reader (Molecular Devices). The specificity of variantproteases at each of the P4-P2 extended subsites is determined by thefluorescence of each of the arrayed amino acids in the P4-P2 PSSClibraries.

Result. Screening by PSSCL confirms that wildtype MT-SP1 has apreference for basic (Arg, Lys) at the P4 and P3 positions, in agreementwith published data by Takeuchi et al., J. Biol. Chem., Vol. 275, Issue34, 26333-26342, Aug. 25, 2000. However, the PSSCL profile also revealsthat its specificity is somewhat broad, such that a variety of aminoacids will be accepted in the P4 and P3 positions in addition to Arg orLys (FIG. 2A). A number of mutants were generated (see above) to narrowthe substrate specificity and to direct it towards potential cleavagesites identified in the VEGF receptor (see below). One mutant, L172D(CB18), shows a very narrow specificity profile, such that Arg or Lys isstrongly preferred over any other amino acid in the P4 and P3 positions(FIG. 2B). A potential cleavage sequence has been identified in VEGFR2(RRVR) that closely matches the specificity profile for L172D (RRXR).Variants of MT-SP1 have been profiled with the P1-Arg PSSCL (forspecific variants, see Table 11). All variants show an increase inselectivity at one or more substrate sequence positions. Representativeprofiles are shown in FIGS. 2A through H.

Example 5 Selection of MT-SP1 Variants Capable of Peptide SequenceSpecific Target Cleavage Using Protease Phage Display

The phagemid is constructed such that it (i) carries all the genesnecessary for M13 phage morphogenesis; (ii) it carries a packagingsignal which interacts with the phage origin of replication to initiateproduction of single-stranded DNA; (iii) it carries a disrupted phageorigin of replication; and (iv) it carries an ampicillin resistancegene.

The combination of an inefficient phage origin of replication and anintact plasmid origin of replication favors propagation of the vector inthe host bacterium as a plasmid (as RF, replicating form, DNA) ratherthan as a phage. It can therefore be maintained without killing thehost. Furthermore, possession of a plasmid origin means that it canreplicate independent of the efficient phage-like propagation of thephagemid. By virtue of the ampicillin resistance gene, the vector can beamplified, which in turn increases packaging of phagemid DNA into phageparticles.

Fusion of the MT-SP1 variant gene to either the gene 3 or gene 8 M13coat proteins can be constructed using standard cloning methods. (Sidhu,Methods in Enzymology, 2000, V328, p 333). A combinatorial library ofvariants within the gene encoding MT-SP1 is then displayed on thesurface of M13 as a fusion to the p3 or p8 M13 coat proteins and pannedagainst an immobilized, aldehyde-containing peptide corresponding to thetarget cleavage of interest. The aldehyde moiety will inhibit theability of the protease to cleave the scissile bond of the protease,however, this moiety does not interfere with protease recognition of thepeptide. Variant protease-displayed phage with specificity for theimmobilized target peptide will bind to target peptide coated plates,whereas non-specific phage will be washed away. Through consecutiverounds of panning, proteases with enhanced specificity towards thetarget sequence can be isolated. The target sequence can then besynthesized without the aldehyde and isolated phage can be tested forspecific hydrolysis of the peptide.

Example 6 Identification of MT-SP1 Mutein Cleavage in the Stalk Regionof VEGFR2

The polypeptide sequence of VEGF receptor 2 (VEGF-R2/KDR), showing therespective sequences of the extracellular (SEQ ID NO:8) andintracellular (SEQ ID NO:9) domains, is provided in Table 12. Sequencesthat closely match the P4-P1 native substrate specificity of MT-SP1 areshown in bold. Two sequences match the recognition profile of both L172Dand wild-type MT-SP1: the boxed sequence RVRK (SEQ ID NO: 13) and thedouble underlined sequence RRVR (SEQ ID NO: 14).

TABLE 12 VEGFR2/KDR Substrate Specificity of Targeted MT-SP1 Proteases

Purified extracellular domain of VEGF-R2 (Flk1) fused to the Fc domainof mouse IgG (2.5 μg) was resuspended with 1 μM MT-SP1 and variantproteases in 17.1 uL of MTSP activation buffer. The reaction wasincubated at 37° C. for 2 hours, deglycosylated with PNGaseF, andseparated by SDS-PAGE electrophoresis. Full length Flk1-Fc and cleavageproducts were identified by staining with Coomassie brilliant blue andthe N-termini sequenced by the Edman protocol. Purified VEGFR2-Fc iscleaved by wild-type and mutant MT-SP1 at the sequence RRVR (SEQ ID NO:14)/KEDE (SEQ ID NO: 19) in the extracellular stalk region of thereceptor. Thus, the present invention provides proteases that can cleavethe VEGFR in the stalk region, and in one embodiment of the invention,such proteases are administered to a patient in need of treatment forcancer, macular degeneration, or another disease in which angiogenesisplays a causative or contributive role.

Example 7 Assaying Cleavage of Purified VEGF Receptor

Purified extracellular domain of VEGF-R2 fused to the Fc domain of mouseIgG (3-10 μg) is resuspended in MTSP activation buffer (20 μL). Variantproteases are added to a final concentration of 100 nM to 1 μM. Thereaction is incubated at 37° C. for 1-2 hours and then separated bySDS-PAGE electrophoresis. Bands are visualized by Coomassie bluestaining, silver staining, and/or Western blot.

Result. The purified VEGFR2-Fc is efficiently cleaved by wild-type andmutant MT-SP1 (FIG. 3). Cleavage by variant proteases yields cleavageproducts with apparent molecular weights of ˜80 kDa and 30 kDa; analysisof potential cleavage sites in VEGFR2 suggests that MT-SP1 variantstarget the stalk (membrane proximal) region of VEGFR2. The mutant L172Dcleaves full-length VEGFR2 but at a reduced rate compared to thewild-type. Several mutants (Q175D and D217F) cleave the receptor withhigher efficiency than wild-type. None of the protease variants orwild-type cleave the Fc domain.

Example 8 Assaying for Cleavage of VEGF Receptor from Endothelial Cells

Human umbilical vein endothelial cells (HUVECs) were purchased fromCambrex and cultured in EBM-2 (endothelial cell basal medium, Cambrex)with full supplements including 2% fetal calf serum (FCS) andantimycotics-antibiotics. For survival assays, cells were plated at adensity of 2×10⁵ cells/ml in EBM-2 into 96-well plates overnight. Thenext day, cells were serum-starved by replacing the media with DMEM+10%FCS for 24 hours. Proteases were then added at varying concentrationsfrom 10-1000 nM and the cells were incubated in the presence of theproteases for 2 hours. VEGF was added at a final concentration of 20ng/mL and the cells were incubated for 72 hours. At the end of the 72hours, cell count was determined by MTT assay (Sigma) according to themanufacturer's protocol.

To visualize the cleavage of the VEGF receptor from the surface ofendothelial cells, cells were grown to ˜70% confluence in 24-wellplates, at which point the media was removed and 200 uL of DMEM plus 10%FCS was added to each well. Proteases to be tested were added at finalconcentrations of 100-1000 nM. Cells were incubated in the presence ofthe proteases for 1-3 hours and the media was removed. Cells were washedwith 1 mL ice cold PBS (3 times) and were scraped off the plate using apipette tip. The resuspended cells were centrifuged at 5000 rpm and thesupernatant was removed. The cells were lysed in 50 uL lysis buffer(PBS+0.1% NP40) by three freeze-thaw cycles on dry ice. The cellsolution was centrifuged at 15,000 rpm to remove membranes andorganelles, and 30 uL of the supernatant was separated by SDS gelelectrophoresis. Proteins were transferred to a PVDF membrane and probedwith an anti-VEGFR2 antibody recognizing the intracellular domain(Chemicon).

Release of the soluble VEGF receptor from the surface of endothelialcells by proteolytic cleavage was detected using a sandwich ELISA.HUVECs were grown in 24-well plates and treated with proteases asdescribed above. After 3 hours incubation, 100 uL of media was removedand the protease inhibitor Pefabloc (Roche) was added to a finalconcentration of 1 mg/mL. The media was then added to Maxisorp plates(Nunc) that had been treated with a monoclonal antibody recognizing theextracellular domain of VEGFR2 (MAB3573, R & D Systems, 1:125 dilutionin PBS). After 1 hour incubation, the plates were washed with PBS+0.01%Tween 20 (PBST), and were treated with a biotinylated polyclonalantibody also recognizing the extracellular domain (BAF357, R & DSystems, 1:500 dilution). After 1 hour incubation, plates were washedwith PBST and then treated with streptavidin conjugated horseradishperoxidase (Upstate). Plates were incubated for 1 hour and then washedwith PBST, and developed using TMB substrate (Amersham) according to themanufacturer's protocol.

Results. Wildtype MTSP and the more specific mutants, including CB18,CB83 and CB152, efficiently inhibited VEGF-dependent proliferation ofendothelial cells in a dose-dependent manner (FIG. 7A). Consistent withthe prediction that the MTSP variants inhibit VEGF-dependent cellproliferation by inactivating the VEGF receptor, FIG. 7B shows that theMTSP variants cleave the VEGF receptor on the surface of endothelialcells. Shown is a Western blot in which HUVECs are incubated with thebuffer control or MTSP variants, and then cell extracts are probed withan antibody recognizing the intracellular domain of VEGFR2. Wild-typeMTSP and variants cleave the full-length receptor (upper band) togenerate a truncated form (lower band). In addition, the extracellulardomain (ectodomain) of the cleaved receptor can be detected in themedia, as shown by the ELISA in FIG. 7C; the released ectodomain isdetectable in samples treated with MTSP and variants, but not in thecontrol.

Example 9 Cornea Micropocket Model

To determine the acute maximum tolerated dose, escalating doses ofpurified wild-type and variant MTSPs were injected i.v. into C57BL/6mice. The mice were observed for outward signs of toxicity and death.

For the cornea micropocket assay, C57BL/6 mice are anesthetized withavertin i.p. and the eye was treated with topical proparacaine.HCl(Allergan, Irvine, Calif.). Hydron/sucralfate pellets containingVEGF-A₁₆₅ (100 ug, R & D Systems) were implanted into a cornealmicropocket at 1 mm from the limbus of both eyes under an operatingmicroscope (Zeiss) followed by intrastomal linear keratotomy by using amicroknife (Medtroni Xomed, Jacksonville, Fla.). A corneal micropocketwas dissected toward the limbus with a von Graefe knife #3 (2×30 mm),followed by pellet implantation and application of topical erythromycin.After 8 days, neovascularization is quantitated by using a slit lampbiomicroscope and the formula 2π×(vessel length/10)×(clock hours). Pvalues were determined by using a two-tailed t test assuming unequalvariances (Microsoft EXCEL). Varying doses of proteases were injected byi.p. twice a day at 12 hour intervals starting at day 0 until day 7.

Results. Wild-type MT-SP1 was well tolerated by mice, with an acutemaximum tolerated dose (MTD) determined to be 50 mg/kg (FIG. 8).Significantly, some of the MT-SP1 variants that were shown to havenarrower selectivity in the profiling libraries (see FIG. 2) were bettertolerated (i.e. had lower toxicities), resulting in higher maximumtolerated doses. CB18 and CB152, for instance, were tolerated at dosesthat resulted in death for wild-type MT-SP1. This demonstrates thatnarrowing the selectivity can be a mechanism for reducing the toxicityof protease drugs.

Wild-type MT-SP1 and variants were tested for their ability to inhibitVEGF-induced angiogenesis in the mouse cornea micropocket model. Asoutlined above, a pellet of VEGF was implanted into the cornea of mice,which is normally avascular, and the amount of neovascularization wasquantitated after 8 days. When mice were treated with either wild-typeor variant MT-SP1, neovascularization was inhibited in a dose dependentmanner (FIG. 9). Treatment of mice with wild-type MT-SP1 at the MTD (50mg/kg) resulted in 42% inhibition of neovascularization. In the case ofCB18, it was possible to dose at a higher concentration due to the lowertoxicity, and at the higher dose (80 mg/kg) an inhibition of 75% wasachieved. Thus, even though wild-type MT-SP1 was effective at inhibitingVEGF-induced angiogenesis, better efficacy was obtained with CB18 due tothe fact that it could be dosed at a higher level.

Example 10 Miles Assay for Vascular Permeability

In addition to angiogenesis, VEGF also induces the permeability of bloodvessels, resulting in the leakage of fluids into the surrounding tissue.VEGF-induced vascular permeability was measured using the Miles assay.Briefly, nude (athymic) mice were injected with 0.5% Evan's blue dye(100 μL, in PBS, Sigma) by tail vein injection. One hour after dyeinjection, 100 ng of VEGF in 20 μL PBS was injected intradermally intothe back of the mice in duplicate spots. Vascular permeability isvisualized by the appearance of blue spots at the site of VEGF injectiondue to the leakage of the dye. The extent of vascular permeability canbe measured semi-quantitatively by measuring the area of the blue spots.To determine if they inhibited vascular permeability, wild-type MT-SP1and variants were injected i.p. at varying doses immediately afterinjection of the dye, and the amount of vascular permeability wasdetermined by measuring the area of dye leakage.

Results. Injection of wild-type and variant MT-SP1 resulted indose-dependent inhibition of vascular permeability (FIG. 10). At thehighest dose tested, wild-type MT-SP1 inhibited vascular permeability upto 80%. Similarly, both CB18 and CB152 inhibited vascular permeability,with CB152 showing higher efficacy at the low 10 mg/kg dose thanwild-type (60% inhibition for CB152 compared to 25% inhibition forwildtype). At their highest doses, all three proteases had comparableefficacy to AVASTIN™, an anti-VEGF antibody approved for colon cancer.

Example 11 Tumor Xenograft Model

Murine Lewis lung carcinoma (LLC) cells are passaged on the dorsalmidline of C57BL/6 mice or in DMEM/10% FCS/penicillin/streptomycin(PNS)/L-glutamine. T241 murine fibrosarcoma is grown in DMEM/10%FCS/PNS/L-glutamine and human pancreatic BxPc3 adenocarcinoma in RPMImedium 1640/10% FCS/PNS. Tumor cells (10⁶) are injected s.c. into thedorsal midline of C57BL/6 mice (8-10 weeks old) for murine tumors andsevere combined immunodeficient (SCID) mice for human tumors, grown to100-200 mm³ (typically 10-14 days) to demonstrate tumor take, and 10⁹pfu of protease-encoding adenoviruses or the control adenovirus Ad Fcgiven by i.v. tail-vein injection. Tumor size in mm³ is calculated bycaliper measurements over a 10- to 14-day period by using the formula0.52×length (mm)×width (mm), using width as the smaller dimension. See,e.g., Kuo et al., PNAS, 2001, 98:4605-4610. P values were determined byusing a two-tailed t test assuming unequal variances (Microsoft EXCEL).

Results. Given that cleavage of VEGFR2 will inactivate the receptor,then the systemic delivery of therapeutically effective amounts ofprotease—either as purified protein or encoded by adenovirus—will resultin inhibition of LLC tumor growth. Failure to inhibit tumor growth maybe due to the inactivation of the protease by endogenous proteaseinhibitors (serpins). In such an event, the covalent binding of theserpin to the protease will be detectable as an increase in size of theprotease by SDS-PAGE. Mutations can be made in the protease that willmake it resistant to serpin inactivation.

Example 12 VEGFR Cleavage

As shown in FIG. 1, scaffold proteases and variants have beensuccessfully expressed as active proteases in yeast or bacterialexpression systems at multi-milligram quantities. See, e.g., protocolsdescribed in Harris 1998 and Takeuchi, 2000. MT-SP1 was engineered toobtain muteins that selectively cleave Flk-1/KDR.

Additional MT-SP1 muteins, shown in Table 11, were cloned and expressedas described above. As shown in FIG. 1, MT-SP1 variants were expressedin bacteria and purified from inclusion bodies. Each protease retainshigh catalytic activity and is >99% pure making them appropriate forcrystallographic studies.

Table 13 depicts the potential target cleavage sequences for wild-typeand mutein MT-SP1. In the table, “Hyd” represents any hydrophobic aminoacid (i.e. glycine, alanine, valine, leucine, isoleucine, phenylalanine,tyrosine, or tryptophan), and “Xxx” represents any amino acid.

TABLE 13 Potential MT-SP1 Cleavage Sequences P4 P3 P2 P1 SEQ ID NOMT-SP1 Native K/R — Hyd — Xxx — K/R 10 specificity Hyd — K/R — Xxx — K/R11 VEGFR2 K — V — G — R 12 sequences R — V — R — K 13 R — R — V — R 14 R— K — T — K 15 K — T — K — K 16 T — K — K — R 17

Example 13 Muteins Consisting of One, Two and Three Mutations withIncreased Selectivity Towards VEGFR Stalk Region Sequence, RRVR

Multiple muteins were characterized by PSSCL profiling showing increasedselectivity towards the RRVR (SEQ ID NO: 14) target cleavage sequence(FIGS. 2A-H). They were grouped into two sub-classes based on whichsubsite profile was most affected by the mutation: P2 or P3&P4.Mutations of Phe99 to Ala, Ile, and Val increased the protease's P2selectivity towards Val, and reduced the specificity of Ala containingsubstrates. This effect is seen in the variants F99V MT-SP1 (CB38), andF99I/L172D/Q175D MT-SP1 (CB159) (FIGS. 2C&D). Mutations such as Phe99 toTrp, Asn, Asp, Ala, or Arg increased the P2 selectivity for Ala, Ser,Trp, Lys and Ile containing substrates. Additional mutations thataffected the P2 selectivity were Met180 to Glu and Ala and Trp215 to Tyrand Phe.

Mutation of Gln192 to Arg and Glu altered the P3 selectivity alone.Mutations at Tyr 146 (Asp), Leu172 (Asp), Gln175 (Asp), Lys224 (Phe),and Met180 (Glu) increased the selectivity of the variants towards bothP3 and P4 Arg and Lys containing substrates as in variant L172D (CB18)(FIG. 2B). Grouping these individual mutations together resulted invariant proteases with highly selective P3 and P4 profiles, such as thevariants L172D/Q175D (CB83) and Y146D/K224F (CB155) (FIGS. 2E&F).

Results. By grouping mutations identified individually to narrow theprotease selectivity at P2 and at P3/P4, multiple variants were madethat had greater than four fold selectivity towards Arg and Lys residuesat the P3 and P4 positions, and altered P2 specificity. Two variantsF99V/L172D/Q175D (CB151) and F99V/K224F (CB152) are at least 3 fold moreselective of Arg and Lys than other amino acids at the P3 and P4subsites, and twice as selective for Val over Ala at the P2 subsite(FIGS. 2G&H). These characteristics in the PSSCL demonstrate theefficacy of mutations from Table 10 on altering the selectivity of theMT-SP1 protease towards the desired RRVR sequence.

Example 14 Screening for Preferential Cleavage of RRVR Versus RQARSubstrates

Mutant proteases that match the desired specificity profiles, asdetermined by substrate libraries, were assayed using individual peptidesubstrates corresponding to the desired cleavage sequence to determinethe magnitude of the change in selectivity. Two substrates weredesigned: Ac-RRVR (SEQ ID NO:14)-AMC and Ac-RQAR (SEQ ID NO: 18)-AMC.The second sequence, RQAR, is a preferred sequence of MT-SP1 asdetermined by substrate profiling. It also matches the sequence in thefull length protease that must be cleaved for protease activation.

Michealis-Menton kinetic constants were determined by the standardkinetic methods. Briefly, the substrate is diluted in a series of 12concentrations between 1 mM and 2 μM in 50 μL total volume of MT-SP1activity buffer in the wells of a Costar 96 well black half-area assayplate. The solution is warmed to 30° C. for five minutes, and 50 μL of aprotease solution between 0.1 and 20 nM was added to the wells of theassay. The fluorescence was measured in a fluorescence spectrophotometer(Molecular Devices Gemini XPS) at an excitation wavelength of 380 nm, anemission wavelength of 450 nm and using a cut-off filter ser at 435 nm.The rate of increase in fluorescence was measured over 30 minutes withreadings taken at 30 second intervals. The kinetic constants k_(cat),K_(m) and k_(cat)/K_(m) were calculated by graphing the inverse of thesubstrate concentration versus the inverse of the velocity of substratecleavage, and fitting to the Lineweaver-Burk equation(1/velocity=(K_(m)/V_(max))(1/[S])+1/V_(max); whereV_(max)=[E]*k_(cat)). The specificity constant (k_(cat)/K_(m)) is ameasure of how well a substrate is cut by a particular protease.

Results: The specificity constants (kcat/Km) for wild type MT-SP1 andseven variants (FIG. 6) demonstrate that the semi-quantitative resultsfor relative selectivity between RQAR (SEQ ID NO: 18) and RRVR (SEQ IDNO: 14) derived from the PSSCL are consistent when measured forindividual substrates. The wild-type protease, MT-SP1, prefers the RQAR(SEQ ID NO: 18) substrate two times more than the RRVR (SEQ ID NO: 14)substrate. Five of the six variant proteases prefer the target sequenceRRVR (SEQ ID NO: 14) over RQAR (SEQ ID NO: 18). Two variants, CB152 andCB159, prefer RRVR (SEQ ID NO: 14) to RQAR (SEQ ID NO: 18) by greaterthan 8 fold. The only exception is CB38 where the profile suggested thatthe selectivity was exclusively at the P4 subsite. In addition to therelative preference of RQAR (SEQ ID NO: 18) versus RRVR (SEQ ID NO: 14),individual substrate kinetic measurements define the efficiency ofsubstrate cleavage for each variant. The variants CB155 and CB159 cutthe Ac-RRVR (SEQ ID NO: 14)-AMC substrate at 2.2 and 2.3×105 M-1s-1,respectively (FIG. 6). These rates are within 3 fold of the wild type,MT-SP1.

Example 15 Screening for Cleavage of Individual Substrates

Mutant proteases that match the desired specificity profiles, asdetermined, for example, by substrate libraries, are assayed usingindividual peptide substrates corresponding to the desired cleavagesequence. Individual kinetic measurements are performed using aSpectra-Max Delta fluorimeter (Molecular Devices). Each protease isdiluted to between 50 nM and 1 μM in assay buffer. All ACC substratesare diluted with MeSO to between 5 and 500 μM, while AMC [DEFINED]substrates are diluted to between 20 and 2000 μM. Each assay containsless than 5% MeSO. Enzymatic activity is monitored every 15 seconds atexcitation and emission wavelengths of 380 nm and 460 nm, respectively,for a total of 10 minutes. All assays are performed in 1% DMSO.

Example 16 Screening for Cleavage of Full-Length Proteins

Variant proteases are assayed to ascertain that they will cleave thedesired sequence when presented in the context of the full-lengthprotein, and the activity of the target protein is assayed to verifythat its function has been destroyed by the cleavage event. The cleavageevent is monitored by SDS-PAGE after incubating the purified full-lengthprotein with the variant protease. The protein is visualized usingstandard Coomasie blue staining, by autoradiography using radio labeledprotein, or by Western blot using the appropriate antibody.Alternatively, if the target protein is a cell surface receptor, cellsexpressing the target protein are exposed to the variant protease. Thecleavage event is monitored by lysing the cells and then separating theproteins by SDS-PAGE, followed by visualization by Western blot.Alternatively, the soluble receptor released by proteolysis isquantified by ELISA.

Cleavage of VEGF.

Vascular endothelial growth factor (VEGF) is an endothelialcell-specific mitogen normally produced during embryogenesis and adultlife. VEGF is a significant mediator of angiogenesis in a variety ofnormal and pathological processes, including tumor development. Threehigh affinity cognate receptors to VEGF have been identified:VEGFR-1/Flt-1, VEGFR-2/KDR, and VEGFR-3/Flt-4.

To determine if MT-SP1 cleaves both the signaling molecule in additionto the receptor, a 165 amino acid recombinant version of VEGF, VEGF165,was assayed by SDS-PAGE. VEGF165 was reconstituted in PBS to aconcentration of 0.2 μg/μL and diluted to a final concentration of 5 μM.Solutions with no protease and 100 nM MT-SP1 or CB152 were incubatedwith the VEGF at 37° C. for five hours. The resulting protein cleavageproducts were deglycosylated, separated by SDS-PAGE, and silver stained(FIG. 11). MT-SP1 efficiently cleaves VEGF165 under the assay conditionswhile the more selective variant CB152 does not. This resultdemonstrates that wild-type MT-SP1 can be used to block VEGF signalingthrough two different mechanisms: cleavage of the mitogen and cleavageof the receptor. CB152, a variant with narrow selectivity to the RRVR(SEQ ID NO: 14) sequence in the stalk region of VEGFR2, does not cleaveVEGF, but does cleave VEGFR and can be dosed at higher concentrationsdue to reduced toxicity.

Cleavage of VEGFR.

¹²⁵I-VEGFR (40,000 cpm) is incubated with varying concentrations ofprotease, samples are boiled in SDS-PAGE sample buffer and examined on a12% polyacrylamide gel. The gels are dried and exposed to x-ray film(Kodak) at −70° C.

VEGFR Binding Assay.

¹²⁵I-VEGFR or PMN are incubated with varying concentrations of proteasesas above. The binding of ¹²⁵I-VEGFR exposed to proteases to normal PMN,or the binding of normal ¹²⁵I-VEGFR to PMN exposed to proteases, arequantified using scintillation. Briefly, 10⁵ cells are incubated withvarying concentrations of ¹²⁵I-VEGFR in 96-well filter plates(Millipore) in the presence of protease inhibitors. Cells are washedthree times by vacuum aspiration and 30 μL of scintillation fluid(Wallac) are added to each well. Scintillation are counted on a WallacMicrobeta scintillation counter (adapted from van Kessel et al., J.Immunol. (1991) 147: 3862-3868 and Porteau et al., JBC (1991)266:18846-18853).

Example 17 Measuring Activity of MT-SP1 in Serum

The activity of MT-SP1 and trypsin was assayed in the presence ofincreasing concentrations of fetal calf serum. The high concentrationsof macromolecular protease inhibitors present in serum makes it a goodin vitro system to test whether a protease would be active in vivo. MTSPand trypsin were resuspended in Dulbecco's Modified Eagle's Medium(DMEM) at 100 nM and 80 nM, respectively, with increasing serumconcentrations (0-10%) in a final volume of 100 μL. A fluorogenicpeptide substrate (Leu-Val-Arg-aminomethylcoumarin) was added to a finalconcentration of 15 μM and fluorescence was detected in a fluorescenceplate reader (Molecular Devices) with an excitation wavelength of 380 nmand an emission wavelength of 460 nm.

As shown in FIG. 5, trypsin shows very strong activity in 0% serum, withthe enzyme using up all the substrate after ˜400 seconds. However, evenin the lowest concentration of serum (2.5%), trypsin activity isdrastically reduced, presumably due to the binding of macromolecularprotease inhibitors. MT-SP1, on the other hand, shows virtually the sameactivity in all concentrations of serum, suggestive that there are noendogenous protease inhibitors in serum that inactivate MT-SP1.

EQUIVALENTS

Although particular embodiments have been disclosed herein in detail,this has been done by way of example for purposes of illustration only,and is not intended to be limiting with respect to the scope of theappended claims, which follow. In particular, it is contemplated by theinventors that various substitutions, alterations, and modifications maybe made to the invention without departing from the spirit and scope ofthe invention as defined by the claims. The choice of screening method,protease scaffold, or library type is believed to be a matter of routinefor a person of ordinary skill in the art with knowledge of theembodiments described herein. Other aspects, advantages, andmodifications considered to be within the scope of the following claims.

1. A mutein membrane type serine protease 1 (MT-SP1) protease that comprises at least one mutation in a scaffold MT-SP1 polypeptide, whereby the substrate specificity or activity of the mutein MT-SP1 polypeptide is altered compared to the scaffold MT-SP1 polypeptide, wherein: the scaffold MT-SP1 polypeptide comprises a sequence of amino acids that is at least 95% identical or is identical to the amino acid sequence of a wild type MT-SP1 whose sequence is set forth in SEQ ID NO:1 or SEQ ID NO:2 or is a species variant of the wild type MT-SP1 of SEQ ID NO:1, or is a catalytically active portion thereof; the mutein MT-SP1 comprises a mutation at a position selected from among amino acid positions 41, 146, 151, 169, 170, 172, 173, 175, 176, 177, 178, 179, 181, and 224; and the numbering is for chymotrypsin.
 2. The mutein MT-SP1 protease of claim 1, wherein the mutein MT-SP1 comprises a mutation at a position selected from among 146, 172, 175 and
 224. 3. The mutein MT-SP1 protease of claim 1, wherein the scaffold MT-SP1 polypeptide comprises the sequence of amino acids set forth in SEQ ID NO:1 or SEQ ID NO:2 or a catalytically active portion thereof.
 4. The mutein MT-SP1 protease of claim 2, wherein the scaffold MT-SP1 polypeptide comprises the sequence of amino acids set forth in SEQ ID NO:1 or SEQ ID NO:2 or a catalytically active portion thereof.
 5. The mutein MT-SP1 protease of claim 1, wherein the sequence of the scaffold protease is set forth in SEQ ID NO:1 or is a catalytically active portion thereof.
 6. The mutein MT-SP1 protease of claim 1, wherein the sequence of the scaffold protease is set forth in SEQ ID NO:2 or is a catalytically active portion thereof.
 7. A pharmaceutical composition, comprising a mutein MT-SP1 protease of claim
 1. 8. The mutein MT-SP1 protease of claim 2, wherein the mutation is selected from among mutations corresponding to Y146F, Y146N, Y146D, Y146E, Y146A, Y146W, Y146R, L172N, L172D, L172E, L172A, L172V, L172F, L172R, Q175D, Q175E, Q175A, Q175V, Q175F, Q175R, K224A, K224F, K224V and K224D.
 9. The mutein MT-SP1 protease of claim 8, wherein the scaffold MT-SP1 polypeptide comprises the sequence of amino acids set forth in SEQ ID NO:1 or SEQ ID NO:2 or a catalytically active portion thereof.
 10. The mutein MT-SP1 of claim 9, further comprising an additional mutation selected from among mutations corresponding to Y146F, Y146N, Y146D, Y146E, Y146A, Y146W, Y146R, L172N, L172D, L172E, L172A, L172V, L172F, L172R, Q175D, Q175E, Q175A, Q175V, Q175F, Q175R, K224A, K224F, K224V, and K224D.
 11. The mutein MT-SP1 protease of claim 10, comprising mutations selected from among the mutations corresponding to L172D/Q175D, Y146D/K224F, or Y146D/L172D/Q175D.
 12. The mutein MT-SP1 of claim 10, wherein the scaffold MT-SP1 polypeptide comprises the sequence of amino acids set forth in SEQ ID NO:1 or SEQ ID NO:2.
 13. The mutein MT-SP1 protease of claim 8, further comprising one or more additional mutations.
 14. The mutein MT-SP1 protease of claim 13, wherein an additional mutation is selected from among mutations corresponding to Y146F, Y146N, Y146D, Y146E, Y146A, Y146W, Y146R, L172N, L172D, L172E, L172A, L172V, L172F, L172R, Q175D, Q175E, Q175A, Q175V, Q175F, Q175R, K224A, K224F, K224V, and K224D.
 15. The mutein MT-SP1 protease of claim 14, wherein at least one mutation is selected from among L172D, Y146F, Q175D and K224F.
 16. The mutein MT-SP1 protease of claim 15, wherein the mutein MT-SP1 has the amino acid mutation K224F.
 17. The mutein MT-SP1 protease of claim 14, comprising mutations selected from among the mutations corresponding to L172D/Q175D, Y146D/K224F or Y146D/L172D/Q175D. 